CRAN Package Check Results for Package MGRASTer

Last updated on 2022-04-28 05:51:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9 2.04 35.66 37.70 NOTE
r-devel-linux-x86_64-debian-gcc 0.9 1.90 27.64 29.54 NOTE
r-devel-linux-x86_64-fedora-clang 0.9 46.23 ERROR
r-devel-linux-x86_64-fedora-gcc 0.9 44.42 ERROR
r-devel-windows-x86_64 0.9 14.00 52.00 66.00 NOTE
r-patched-linux-x86_64 0.9 2.63 35.32 37.95 NOTE
r-release-linux-x86_64 0.9 1.84 34.82 36.66 NOTE
r-release-macos-arm64 0.9 15.00 NOTE
r-release-macos-x86_64 0.9 27.00 NOTE
r-release-windows-x86_64 0.9 5.00 51.00 56.00 NOTE
r-oldrel-macos-arm64 0.9 22.00 NOTE
r-oldrel-macos-x86_64 0.9 29.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9 5.00 43.00 48.00 NOTE

Check Details

Version: 0.9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to 'RJSONIO' in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9
Check: R code for possible problems
Result: NOTE
    .onAttach: no visible global function definition for 'packageVersion'
    .onAttach: no visible binding for global variable '.MGRAST'
    build.MGRAST: no visible binding for global variable '.MGRAST'
    build.MGRAST: no visible global function definition for 'fromJSON'
    call.MGRAST: no visible binding for global variable '.MGRAST'
    call.MGRAST: no visible global function definition for 'download.file'
    call.MGRAST: no visible global function definition for 'isValidJSON'
    call.MGRAST: no visible global function definition for 'fromJSON'
    doc.MGRAST: no visible binding for global variable '.MGRAST'
    doc.MGRAST: no visible global function definition for 'str'
    load.MGRAST: no visible binding for global variable '.MGRAST'
    parse.MGRAST: no visible binding for global variable '.MGRAST'
    this.package: no visible binding for global variable '.MGRAST'
    Undefined global functions or variables:
     .MGRAST download.file fromJSON isValidJSON packageVersion str
    Consider adding
     importFrom("utils", "download.file", "packageVersion", "str")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9
Check: tests
Result: ERROR
     Running ‘tests.R’
    Running the tests in ‘tests/tests.R’ failed.
    Complete output:
     > ##############################################################################
     > #
     > # Although this package is essentially a wrapper for a distinct API,
     > # the design is intended to ensure stability with respect to the R platform,
     > # independent of changes to that API.
     > #
     > # The MG-RAST API is developed in a dynamic environment. Our goal here is
     > # for package functionality to handle well in the face of significant API changes,
     > # patches, hotfixes, etc.
     > #
     > # (Of course, this only applies to interim periods between package versions,
     > # which do regularly incorporate latest API updates.)
     > #
     > # In particular, these package tests test the package, not the API. They are
     > # written with the thought that the package will still "work" in a formal sense,
     > # even when the API does not. This refers to buggy behavior, s as well as
     > # occasional server downtime.
     > #
     > # The effort made to accommodate API updates dynamically is par of this approach,
     > # comprised of the build.MGRAST() and load.MGRAST() functions. They can only
     > # provide so much resilience, of course.
     > #
     > # One of the challenges of this project has been that, although the API
     > # is formally specified, best results in practice have required experimentation
     > # and been modeled on examples.
     > #
     > # Accordingly, these URLs from API documentation form the backbone of testing.
     > # Some are also copied to the doc examples of call.MGRAST() and parse.MGRAST().
     > # Updates here may require updates there. Last updated April 2014.
     > #
     > # Per correspondence with CRAN, the policy in these tests is not to actually
     > # attempt communicaton with the MG-RAST API server. Such tests are present
     > # below in comments, however.
     > #
     > #
     > # http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt
     > # http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO
     > # http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order
     > # http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1
     > # http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650
     > # http://api.metagenomics.anl.gov/library?limit=20&order=name
     > # http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full
     > # http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3
     > # http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus
     > # http://api.metagenomics.anl.gov/m5nr/sources
     > # http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1
     > # http://api.metagenomics.anl.gov/m5nr/alias/IPR001478
     > # http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro
     > # http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank
     > # http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG
     > # http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL
     > # http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15
     > # http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes
     > # http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25
     > # http://api.metagenomics.anl.gov/metadata/template
     > # http://api.metagenomics.anl.gov/metadata/cv
     > # http://api.metagenomics.anl.gov/metadata/export/mgp128
     > # http://api.metagenomics.anl.gov/metagenome?limit=20&order=name
     > # http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata
     > # http://api.metagenomics.anl.gov/project?limit=20&order=name
     > # http://api.metagenomics.anl.gov/project/mgp128?verbosity=full
     > # http://api.metagenomics.anl.gov/sample?limit=20&order=name
     > # http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full
     > # http://api.metagenomics.anl.gov/validation/template/
     > # http://api.metagenomics.anl.gov/validation/data/?template=
     > #
     > ##############################################################################
     >
     >
     > library(MGRASTer)
     MGRASTer (0.9 02e288)
     >
     > #-----------------------------------------------------------------------------
     > # test package environment & local API representation.
     > # also, test access and slicing of documentation.
     > # we would like a simpler way to list controlled vocabularies
     > # than the last two examples, but that must wait.
     > #-----------------------------------------------------------------------------
     >
     > ls (.MGRAST)
     [1] "API" "API.version" "server" "this.package"
     > get ("server", envir=.MGRAST)
     [1] "http://api.metagenomics.anl.gov"
     > get ("this.package", envir=.MGRAST)
     name
     "MGRASTer"
     > get ("API.version", envir=.MGRAST)
     [1] "1"
     > get ("API", envir=.MGRAST)
     $annotation
     $annotation$info
     $annotation$info$parameters
     $annotation$info$parameters$body
     named list()
    
     $annotation$info$parameters$options
     named list()
    
     $annotation$info$parameters$required
     named list()
    
    
     $annotation$info$request
     [1] "http://api.metagenomics.anl.gov/annotation"
    
     $annotation$info$name
     [1] "info"
    
     $annotation$info$type
     [1] "synchronous"
    
     $annotation$info$method
     [1] "GET"
    
     $annotation$info$attributes
     [1] "self"
    
     $annotation$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $annotation$sequence
     $annotation$sequence$request
     [1] "http://api.metagenomics.anl.gov/annotation/sequence/{ID}"
    
     $annotation$sequence$example
     [1] "http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
     [2] "all annotated read sequences from mgm4447943.3 with hits in SwissProt organisms at evaule < e-10"
    
     $annotation$sequence$name
     [1] "sequence"
    
     $annotation$sequence$description
     [1] "tab deliminted annotated sequence stream"
    
     $annotation$sequence$parameters
     $annotation$sequence$parameters$body
     named list()
    
     $annotation$sequence$parameters$options
     $annotation$sequence$parameters$options$source
     $annotation$sequence$parameters$options$source[[1]]
     [1] "cv"
    
     $annotation$sequence$parameters$options$source[[2]]
     $annotation$sequence$parameters$options$source[[2]][[1]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[2]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[3]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[4]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[5]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[6]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[7]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[8]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[9]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[10]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[11]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[12]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$sequence$parameters$options$source[[2]][[13]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $annotation$sequence$parameters$options$source[[2]][[14]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $annotation$sequence$parameters$options$source[[2]][[15]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $annotation$sequence$parameters$options$source[[2]][[16]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $annotation$sequence$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $annotation$sequence$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $annotation$sequence$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $annotation$sequence$parameters$options$filter
     [1] "string"
     [2] "text string to filter annotations by: only return those that contain text"
    
     $annotation$sequence$parameters$options$type
     $annotation$sequence$parameters$options$type[[1]]
     [1] "cv"
    
     $annotation$sequence$parameters$options$type[[2]]
     $annotation$sequence$parameters$options$type[[2]][[1]]
     [1] "organism" "return organism data"
    
     $annotation$sequence$parameters$options$type[[2]][[2]]
     [1] "function" "return function data"
    
     $annotation$sequence$parameters$options$type[[2]][[3]]
     [1] "ontology" "return ontology data"
    
     $annotation$sequence$parameters$options$type[[2]][[4]]
     [1] "feature" "return feature data"
    
     $annotation$sequence$parameters$options$type[[2]][[5]]
     [1] "md5" "return md5sum data"
    
    
    
     $annotation$sequence$parameters$options$filter_level
     [1] "string"
     [2] "hierarchal level to filter annotations by, for organism or ontology only"
    
    
     $annotation$sequence$parameters$required
     $annotation$sequence$parameters$required$id
     [1] "string" "unique metagenome identifier"
    
    
    
     $annotation$sequence$method
     [1] "GET"
    
     $annotation$sequence$type
     [1] "stream"
    
     $annotation$sequence$attributes
     $annotation$sequence$attributes$`streaming text`
     $annotation$sequence$attributes$`streaming text`[[1]]
     [1] "object"
    
     $annotation$sequence$attributes$`streaming text`[[2]]
     $annotation$sequence$attributes$`streaming text`[[2]][[1]]
     $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_02
     [1] "string" "m5nr id (md5sum)"
    
     $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_04
     [1] "string"
     [2] "semicolon seperated list of annotations"
    
     $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_03
     [1] "string" "dna sequence"
    
     $annotation$sequence$attributes$`streaming text`[[2]][[1]]$col_01
     [1] "string" "sequence id"
    
    
     $annotation$sequence$attributes$`streaming text`[[2]][[2]]
     [1] "tab deliminted annotated sequence stream"
    
    
    
    
    
     $annotation$similarity
     $annotation$similarity$request
     [1] "http://api.metagenomics.anl.gov/annotation/similarity/{ID}"
    
     $annotation$similarity$example
     [1] "http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO"
     [2] "all annotated read blat stats from mgm4447943.3 with hits in KO functions at % identity > 80"
    
     $annotation$similarity$name
     [1] "similarity"
    
     $annotation$similarity$description
     [1] "tab deliminted blast m8 with annotation"
    
     $annotation$similarity$parameters
     $annotation$similarity$parameters$body
     named list()
    
     $annotation$similarity$parameters$options
     $annotation$similarity$parameters$options$source
     $annotation$similarity$parameters$options$source[[1]]
     [1] "cv"
    
     $annotation$similarity$parameters$options$source[[2]]
     $annotation$similarity$parameters$options$source[[2]][[1]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[2]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[3]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[4]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[5]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[6]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[7]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[8]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[9]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[10]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[11]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[12]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
     $annotation$similarity$parameters$options$source[[2]][[13]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $annotation$similarity$parameters$options$source[[2]][[14]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $annotation$similarity$parameters$options$source[[2]][[15]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $annotation$similarity$parameters$options$source[[2]][[16]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $annotation$similarity$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $annotation$similarity$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $annotation$similarity$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $annotation$similarity$parameters$options$filter
     [1] "string"
     [2] "text string to filter annotations by: only return those that contain text"
    
     $annotation$similarity$parameters$options$type
     $annotation$similarity$parameters$options$type[[1]]
     [1] "cv"
    
     $annotation$similarity$parameters$options$type[[2]]
     $annotation$similarity$parameters$options$type[[2]][[1]]
     [1] "organism" "return organism data"
    
     $annotation$similarity$parameters$options$type[[2]][[2]]
     [1] "function" "return function data"
    
     $annotation$similarity$parameters$options$type[[2]][[3]]
     [1] "ontology" "return ontology data"
    
     $annotation$similarity$parameters$options$type[[2]][[4]]
     [1] "feature" "return feature data"
    
     $annotation$similarity$parameters$options$type[[2]][[5]]
     [1] "md5" "return md5sum data"
    
    
    
     $annotation$similarity$parameters$options$filter_level
     [1] "string"
     [2] "hierarchal level to filter annotations by, for organism or ontology only"
    
    
     $annotation$similarity$parameters$required
     $annotation$similarity$parameters$required$id
     [1] "string" "unique metagenome identifier"
    
    
    
     $annotation$similarity$method
     [1] "GET"
    
     $annotation$similarity$type
     [1] "stream"
    
     $annotation$similarity$attributes
     $annotation$similarity$attributes$`streaming text`
     $annotation$similarity$attributes$`streaming text`[[1]]
     [1] "object"
    
     $annotation$similarity$attributes$`streaming text`[[2]]
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_08
     [1] "int" "query end"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_12
     [1] "float" "bit score"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_02
     [1] "string" "hit m5nr id (md5sum)"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_05
     [1] "int" "number of mismatches"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_07
     [1] "int" "query start"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_11
     [1] "float" "e-value"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_10
     [1] "int" "hit end"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_04
     [1] "int" "alignment length,"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_06
     [1] "int" "number of gap openings"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_09
     [1] "int" "hit start"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_03
     [1] "float" "percentage identity"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_13
     [1] "string"
     [2] "semicolon seperated list of annotations"
    
     $annotation$similarity$attributes$`streaming text`[[2]][[1]]$col_01
     [1] "string" "query sequence id"
    
    
     $annotation$similarity$attributes$`streaming text`[[2]][[2]]
     [1] "tab deliminted blast m8 with annotation"
    
    
    
    
    
    
     $compute
     $compute$info
     $compute$info$parameters
     $compute$info$parameters$body
     named list()
    
     $compute$info$parameters$required
     named list()
    
     $compute$info$parameters$options
     named list()
    
    
     $compute$info$request
     [1] "http://api.metagenomics.anl.gov/compute"
    
     $compute$info$name
     [1] "info"
    
     $compute$info$type
     [1] "synchronous"
    
     $compute$info$method
     [1] "GET"
    
     $compute$info$attributes
     [1] "self"
    
     $compute$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $compute$alphadiversity
     $compute$alphadiversity$request
     [1] "http://api.metagenomics.anl.gov/compute/alphadiversity/{ID}"
    
     $compute$alphadiversity$example
     [1] "http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order"
     [2] "retrieve alpha diversity for order taxon"
    
     $compute$alphadiversity$name
     [1] "alphadiversity"
    
     $compute$alphadiversity$description
     [1] "Calculate alpha diversity value for given ID and taxon level."
    
     $compute$alphadiversity$parameters
     $compute$alphadiversity$parameters$body
     named list()
    
     $compute$alphadiversity$parameters$required
     $compute$alphadiversity$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $compute$alphadiversity$parameters$options
     $compute$alphadiversity$parameters$options$source
     $compute$alphadiversity$parameters$options$source[[1]]
     [1] "cv"
    
     $compute$alphadiversity$parameters$options$source[[2]]
     $compute$alphadiversity$parameters$options$source[[2]][[1]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[2]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[3]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[4]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[5]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[6]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[7]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[8]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[9]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[10]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[11]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $compute$alphadiversity$parameters$options$source[[2]][[12]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
    
    
     $compute$alphadiversity$parameters$options$level
     $compute$alphadiversity$parameters$options$level[[1]]
     [1] "cv"
    
     $compute$alphadiversity$parameters$options$level[[2]]
     $compute$alphadiversity$parameters$options$level[[2]][[1]]
     [1] "strain" "bottom organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[2]]
     [1] "species" "organism type level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[3]]
     [1] "genus" "organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[4]]
     [1] "family" "organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[5]]
     [1] "order" "organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[6]]
     [1] "class" "organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[7]]
     [1] "phylum" "organism taxanomic level"
    
     $compute$alphadiversity$parameters$options$level[[2]][[8]]
     [1] "domain" "top organism taxanomic level"
    
    
    
    
    
     $compute$alphadiversity$method
     [1] "GET"
    
     $compute$alphadiversity$type
     [1] "synchronous"
    
     $compute$alphadiversity$attributes
     $compute$alphadiversity$attributes$url
     [1] "string"
     [2] "resource location of this object instance"
    
     $compute$alphadiversity$attributes$data
     [1] "float" "alpha diversity value"
    
     $compute$alphadiversity$attributes$id
     [1] "string" "unique metagenome identifier"
    
    
    
    
     $download
     $download$info
     $download$info$parameters
     $download$info$parameters$body
     named list()
    
     $download$info$parameters$required
     named list()
    
     $download$info$parameters$options
     named list()
    
    
     $download$info$request
     [1] "http://api.metagenomics.anl.gov/download"
    
     $download$info$name
     [1] "info"
    
     $download$info$type
     [1] "synchronous"
    
     $download$info$method
     [1] "GET"
    
     $download$info$attributes
     [1] "self"
    
     $download$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $download$instance
     $download$instance$request
     [1] "http://api.metagenomics.anl.gov/download/{ID}"
    
     $download$instance$example
     [1] "http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1"
     [2] "download fasta file of genecalled protein sequences (from stage 350)"
    
     $download$instance$name
     [1] "instance"
    
     $download$instance$description
     [1] "Returns a single sequence file."
    
     $download$instance$parameters
     $download$instance$parameters$body
     named list()
    
     $download$instance$parameters$required
     $download$instance$parameters$required$id
     [1] "string" "unique metagenome identifier"
    
    
     $download$instance$parameters$options
     $download$instance$parameters$options$file
     [1] "string" "file name or identifier"
    
    
    
     $download$instance$method
     [1] "GET"
    
     $download$instance$type
     [1] "synchronous"
    
     $download$instance$attributes
     $download$instance$attributes$data
     [1] "file" "requested analysis file"
    
    
    
     $download$setlist
     $download$setlist$request
     [1] "http://api.metagenomics.anl.gov/download/{ID}"
    
     $download$setlist$example
     [1] "http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650"
     [2] "view all available files from stage 650"
    
     $download$setlist$name
     [1] "setlist"
    
     $download$setlist$description
     [1] "Returns a list of sets of sequence files for the given id."
    
     $download$setlist$parameters
     $download$setlist$parameters$body
     named list()
    
     $download$setlist$parameters$required
     $download$setlist$parameters$required$id
     [1] "string" "unique metagenome identifier"
    
    
     $download$setlist$parameters$options
     $download$setlist$parameters$options$stage
     [1] "string" "stage name or identifier"
    
    
    
     $download$setlist$method
     [1] "GET"
    
     $download$setlist$type
     [1] "synchronous"
    
     $download$setlist$attributes
     $download$setlist$attributes$stage_name
     [1] "string"
     [2] "name of the stage in processing of this file"
    
     $download$setlist$attributes$file_name
     [1] "string" "name of the analysis file"
    
     $download$setlist$attributes$url
     [1] "string"
     [2] "url for retrieving this analysis file"
    
     $download$setlist$attributes$id
     [1] "string" "unique metagenome identifier"
    
     $download$setlist$attributes$file_id
     [1] "string" "unique identifier of file in stage"
    
     $download$setlist$attributes$stage_type
     [1] "string"
     [2] "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
    
     $download$setlist$attributes$stage_id
     [1] "string"
     [2] "three digit numerical identifier of the stage"
    
    
    
    
     $inbox
     $inbox$info
     $inbox$info$parameters
     $inbox$info$parameters$body
     named list()
    
     $inbox$info$parameters$required
     named list()
    
     $inbox$info$parameters$options
     named list()
    
    
     $inbox$info$request
     [1] "http://api.metagenomics.anl.gov/inbox"
    
     $inbox$info$name
     [1] "info"
    
     $inbox$info$type
     [1] "synchronous"
    
     $inbox$info$method
     [1] "GET"
    
     $inbox$info$attributes
     [1] "self"
    
     $inbox$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $inbox$view
     $inbox$view$request
     [1] "http://api.metagenomics.anl.gov/inbox"
    
     $inbox$view$example
     [1] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/inbox\""
     [2] "lists the contents of the user inbox, auth is required"
    
     $inbox$view$name
     [1] "view"
    
     $inbox$view$description
     [1] "lists the contents of the user inbox"
    
     $inbox$view$parameters
     $inbox$view$parameters$body
     named list()
    
     $inbox$view$parameters$required
     $inbox$view$parameters$required$auth
     [1] "string"
     [2] "unique string of text generated by MG-RAST for your account"
    
    
     $inbox$view$parameters$options
     named list()
    
    
     $inbox$view$method
     [1] "GET"
    
     $inbox$view$type
     [1] "synchronous"
    
     $inbox$view$attributes
     $inbox$view$attributes$timestamp
     [1] "string" "timestamp for return of this query"
    
     $inbox$view$attributes$files
     $inbox$view$attributes$files[[1]]
     [1] "list"
    
     $inbox$view$attributes$files[[2]]
     $inbox$view$attributes$files[[2]][[1]]
     [1] "object"
    
     $inbox$view$attributes$files[[2]][[2]]
     $inbox$view$attributes$files[[2]][[2]][[1]]
     $inbox$view$attributes$files[[2]][[2]][[1]]$filesize
     [1] "string" "disk size of file in bytes"
    
     $inbox$view$attributes$files[[2]][[2]][[1]]$timestamp
     [1] "string" "timestamp of file"
    
     $inbox$view$attributes$files[[2]][[2]][[1]]$filename
     [1] "string" "path of file from within user inbox"
    
    
     $inbox$view$attributes$files[[2]][[2]][[2]]
     [1] "list of file objects"
    
    
    
    
     $inbox$view$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $inbox$view$attributes$id
     [1] "string" "user login"
    
    
    
    
     $library
     $library$info
     $library$info$parameters
     $library$info$parameters$body
     named list()
    
     $library$info$parameters$required
     named list()
    
     $library$info$parameters$options
     named list()
    
    
     $library$info$request
     [1] "http://api.metagenomics.anl.gov/library"
    
     $library$info$name
     [1] "info"
    
     $library$info$type
     [1] "synchronous"
    
     $library$info$method
     [1] "GET"
    
     $library$info$attributes
     [1] "self"
    
     $library$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $library$query
     $library$query$request
     [1] "http://api.metagenomics.anl.gov/library"
    
     $library$query$example
     [1] "http://api.metagenomics.anl.gov/library?limit=20&order=name"
     [2] "retrieve the first 20 libraries ordered by name"
    
     $library$query$name
     [1] "query"
    
     $library$query$description
     [1] "Returns a set of data matching the query criteria."
    
     $library$query$parameters
     $library$query$parameters$body
     named list()
    
     $library$query$parameters$required
     named list()
    
     $library$query$parameters$options
     $library$query$parameters$options$verbosity
     $library$query$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $library$query$parameters$options$verbosity[[2]]
     $library$query$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
    
    
     $library$query$parameters$options$order
     $library$query$parameters$options$order[[1]]
     [1] "cv"
    
     $library$query$parameters$options$order[[2]]
     $library$query$parameters$options$order[[2]][[1]]
     [1] "id" "return data objects ordered by id"
    
     $library$query$parameters$options$order[[2]][[2]]
     [1] "name" "return data objects ordered by name"
    
    
    
     $library$query$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $library$query$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $library$query$method
     [1] "GET"
    
     $library$query$type
     [1] "synchronous"
    
     $library$query$attributes
     $library$query$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $library$query$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $library$query$attributes$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $library$query$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $library$query$attributes$data
     $library$query$attributes$data[[1]]
     [1] "list"
    
     $library$query$attributes$data[[2]]
     $library$query$attributes$data[[2]][[1]]
     [1] "object"
    
     $library$query$attributes$data[[2]][[2]]
     $library$query$attributes$data[[2]][[2]][[1]]
     $library$query$attributes$data[[2]][[2]][[1]]$version
     [1] "integer" "version of the object"
    
     $library$query$attributes$data[[2]][[2]][[1]]$project
     [1] "reference project" "reference to the project object"
    
     $library$query$attributes$data[[2]][[2]][[1]]$name
     [1] "string" "human readable identifier"
    
     $library$query$attributes$data[[2]][[2]][[1]]$sequencesets
     $library$query$attributes$data[[2]][[2]][[1]]$sequencesets[[1]]
     [1] "list"
    
     $library$query$attributes$data[[2]][[2]][[1]]$sequencesets[[2]]
     [1] "reference sequenceset"
     [2] "a list of references to the related sequence sets"
    
    
     $library$query$attributes$data[[2]][[2]][[1]]$metagenome
     [1] "reference metagenome"
     [2] "reference to the related metagenome object"
    
     $library$query$attributes$data[[2]][[2]][[1]]$created
     [1] "date" "time the object was first created"
    
     $library$query$attributes$data[[2]][[2]][[1]]$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $library$query$attributes$data[[2]][[2]][[1]]$id
     [1] "string" "unique object identifier"
    
     $library$query$attributes$data[[2]][[2]][[1]]$sample
     [1] "reference sample"
     [2] "reference to the related sample object"
    
     $library$query$attributes$data[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
     $library$query$attributes$data[[2]][[2]][[2]]
     [1] "list of the library objects"
    
    
    
    
     $library$query$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
     $library$query$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
    
    
     $library$instance
     $library$instance$request
     [1] "http://api.metagenomics.anl.gov/library/{ID}"
    
     $library$instance$example
     [1] "http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full"
     [2] "retrieve all data for library mgl52924"
    
     $library$instance$name
     [1] "instance"
    
     $library$instance$description
     [1] "Returns a single data object."
    
     $library$instance$parameters
     $library$instance$parameters$body
     named list()
    
     $library$instance$parameters$required
     $library$instance$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $library$instance$parameters$options
     $library$instance$parameters$options$verbosity
     $library$instance$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $library$instance$parameters$options$verbosity[[2]]
     $library$instance$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $library$instance$parameters$options$verbosity[[2]][[2]]
     [1] "verbose"
     [2] "returns a standard subselection of metadata"
    
     $library$instance$parameters$options$verbosity[[2]][[3]]
     [1] "full" "returns all connected metadata"
    
    
    
    
    
     $library$instance$method
     [1] "GET"
    
     $library$instance$type
     [1] "synchronous"
    
     $library$instance$attributes
     $library$instance$attributes$version
     [1] "integer" "version of the object"
    
     $library$instance$attributes$project
     [1] "reference project" "reference to the project object"
    
     $library$instance$attributes$name
     [1] "string" "human readable identifier"
    
     $library$instance$attributes$sequencesets
     $library$instance$attributes$sequencesets[[1]]
     [1] "list"
    
     $library$instance$attributes$sequencesets[[2]]
     [1] "reference sequenceset"
     [2] "a list of references to the related sequence sets"
    
    
     $library$instance$attributes$metagenome
     [1] "reference metagenome"
     [2] "reference to the related metagenome object"
    
     $library$instance$attributes$created
     [1] "date" "time the object was first created"
    
     $library$instance$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $library$instance$attributes$id
     [1] "string" "unique object identifier"
    
     $library$instance$attributes$sample
     [1] "reference sample"
     [2] "reference to the related sample object"
    
     $library$instance$attributes$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
    
    
     $m5nr
     $m5nr$info
     $m5nr$info$parameters
     $m5nr$info$parameters$body
     named list()
    
     $m5nr$info$parameters$required
     named list()
    
     $m5nr$info$parameters$options
     named list()
    
    
     $m5nr$info$request
     [1] "http://api.metagenomics.anl.gov/m5nr"
    
     $m5nr$info$name
     [1] "info"
    
     $m5nr$info$type
     [1] "synchronous"
    
     $m5nr$info$method
     [1] "GET"
    
     $m5nr$info$attributes
     [1] "self"
    
     $m5nr$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $m5nr$ontology
     $m5nr$ontology$request
     [1] "http://api.metagenomics.anl.gov/m5nr/ontology"
    
     $m5nr$ontology$example
     [1] "http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3"
     [2] "retrieve subsystems hierarchy for the top 3 levels"
    
     $m5nr$ontology$name
     [1] "ontology"
    
     $m5nr$ontology$description
     [1] "Return functional hierarchy"
    
     $m5nr$ontology$parameters
     $m5nr$ontology$parameters$body
     named list()
    
     $m5nr$ontology$parameters$required
     named list()
    
     $m5nr$ontology$parameters$options
     $m5nr$ontology$parameters$options$source
     $m5nr$ontology$parameters$options$source[[1]]
     [1] "cv"
    
     $m5nr$ontology$parameters$options$source[[2]]
     $m5nr$ontology$parameters$options$source[[2]][[1]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $m5nr$ontology$parameters$options$source[[2]][[2]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $m5nr$ontology$parameters$options$source[[2]][[3]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $m5nr$ontology$parameters$options$source[[2]][[4]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $m5nr$ontology$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$ontology$parameters$options$filter
     [1] "string"
     [2] "text of ontology group (filter_level) to filter by"
    
     $m5nr$ontology$parameters$options$exact
     [1] "boolean"
     [2] "if true return only those ontologies that exactly match filter, default is false"
    
     $m5nr$ontology$parameters$options$filter_level
     $m5nr$ontology$parameters$options$filter_level[[1]]
     [1] "cv"
    
     $m5nr$ontology$parameters$options$filter_level[[2]]
     $m5nr$ontology$parameters$options$filter_level[[2]][[1]]
     [1] "function" "bottom function ontology level"
    
     $m5nr$ontology$parameters$options$filter_level[[2]][[2]]
     [1] "level3" "function ontology level"
    
     $m5nr$ontology$parameters$options$filter_level[[2]][[3]]
     [1] "level2" "function ontology level"
    
     $m5nr$ontology$parameters$options$filter_level[[2]][[4]]
     [1] "level1" "top function ontology level"
    
    
    
     $m5nr$ontology$parameters$options$min_level
     $m5nr$ontology$parameters$options$min_level[[1]]
     [1] "cv"
    
     $m5nr$ontology$parameters$options$min_level[[2]]
     $m5nr$ontology$parameters$options$min_level[[2]][[1]]
     [1] "function" "bottom function ontology level"
    
     $m5nr$ontology$parameters$options$min_level[[2]][[2]]
     [1] "level3" "function ontology level"
    
     $m5nr$ontology$parameters$options$min_level[[2]][[3]]
     [1] "level2" "function ontology level"
    
     $m5nr$ontology$parameters$options$min_level[[2]][[4]]
     [1] "level1" "top function ontology level"
    
    
    
    
    
     $m5nr$ontology$method
     [1] "GET"
    
     $m5nr$ontology$type
     [1] "synchronous"
    
     $m5nr$ontology$attributes
     $m5nr$ontology$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$ontology$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$ontology$attributes$data
     $m5nr$ontology$attributes$data[[1]]
     [1] "list"
    
     $m5nr$ontology$attributes$data[[2]]
     $m5nr$ontology$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$ontology$attributes$data[[2]][[2]]
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level4
     [1] "string" "ontology bottom level"
    
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level2
     [1] "string" "ontology level 2"
    
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level3
     [1] "string" "ontology level 3"
    
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$id
     [1] "string" "ontology ID"
    
     $m5nr$ontology$attributes$data[[2]][[2]][[1]]$level1
     [1] "string" "ontology top level"
    
    
     $m5nr$ontology$attributes$data[[2]][[2]][[2]]
     [1] "ontology object"
    
    
    
    
    
    
     $m5nr$taxonomy
     $m5nr$taxonomy$request
     [1] "http://api.metagenomics.anl.gov/m5nr/taxonomy"
    
     $m5nr$taxonomy$example
     [1] "http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus"
     [2] "retrieve all class level taxa that belong to Bacteroidetes"
    
     $m5nr$taxonomy$name
     [1] "taxonomy"
    
     $m5nr$taxonomy$description
     [1] "Return organism hierarchy"
    
     $m5nr$taxonomy$parameters
     $m5nr$taxonomy$parameters$body
     named list()
    
     $m5nr$taxonomy$parameters$required
     named list()
    
     $m5nr$taxonomy$parameters$options
     $m5nr$taxonomy$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$taxonomy$parameters$options$filter
     [1] "string"
     [2] "text of taxanomy group (filter_level) to filter by"
    
     $m5nr$taxonomy$parameters$options$exact
     [1] "boolean"
     [2] "if true return only those taxonomies that exactly match filter, default is false"
    
     $m5nr$taxonomy$parameters$options$filter_level
     $m5nr$taxonomy$parameters$options$filter_level[[1]]
     [1] "cv"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]]
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[1]]
     [1] "species" "organism type level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[2]]
     [1] "genus" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[3]]
     [1] "family" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[4]]
     [1] "order" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[5]]
     [1] "class" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[6]]
     [1] "phylum" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$filter_level[[2]][[7]]
     [1] "domain" "top organism taxanomic level"
    
    
    
     $m5nr$taxonomy$parameters$options$min_level
     $m5nr$taxonomy$parameters$options$min_level[[1]]
     [1] "cv"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]]
     $m5nr$taxonomy$parameters$options$min_level[[2]][[1]]
     [1] "species" "organism type level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[2]]
     [1] "genus" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[3]]
     [1] "family" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[4]]
     [1] "order" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[5]]
     [1] "class" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[6]]
     [1] "phylum" "organism taxanomic level"
    
     $m5nr$taxonomy$parameters$options$min_level[[2]][[7]]
     [1] "domain" "top organism taxanomic level"
    
    
    
    
    
     $m5nr$taxonomy$method
     [1] "GET"
    
     $m5nr$taxonomy$type
     [1] "synchronous"
    
     $m5nr$taxonomy$attributes
     $m5nr$taxonomy$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$taxonomy$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$taxonomy$attributes$data
     $m5nr$taxonomy$attributes$data[[1]]
     [1] "list"
    
     $m5nr$taxonomy$attributes$data[[2]]
     $m5nr$taxonomy$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]]
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$genus
     [1] "string" "organism genus"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi id"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$species
     [1] "string" "organism species"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$domain
     [1] "string" "organism domain"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$order
     [1] "string" "organism order"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$class
     [1] "string" "organism class"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$phylum
     [1] "string" "organism phylum"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism name"
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[1]]$family
     [1] "string" "organism family"
    
    
     $m5nr$taxonomy$attributes$data[[2]][[2]][[2]]
     [1] "taxonomy object"
    
    
    
    
    
    
     $m5nr$sources
     $m5nr$sources$request
     [1] "http://api.metagenomics.anl.gov/m5nr/sources"
    
     $m5nr$sources$example
     [1] "http://api.metagenomics.anl.gov/m5nr/sources"
     [2] "retrieve all data sources for M5NR"
    
     $m5nr$sources$name
     [1] "sources"
    
     $m5nr$sources$description
     [1] "Return all sources in M5NR"
    
     $m5nr$sources$parameters
     $m5nr$sources$parameters$body
     named list()
    
     $m5nr$sources$parameters$required
     named list()
    
     $m5nr$sources$parameters$options
     $m5nr$sources$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
    
    
     $m5nr$sources$method
     [1] "GET"
    
     $m5nr$sources$type
     [1] "synchronous"
    
     $m5nr$sources$attributes
     $m5nr$sources$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$sources$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$sources$attributes$data
     $m5nr$sources$attributes$data[[1]]
     [1] "list"
    
     $m5nr$sources$attributes$data[[2]]
     [1] "object" "source object"
    
    
    
    
     $m5nr$accession
     $m5nr$accession$request
     [1] "http://api.metagenomics.anl.gov/m5nr/accession/{id}"
    
     $m5nr$accession$example
     [1] "http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1"
     [2] "retrieve M5NR data for accession ID 'YP_003268079.1'"
    
     $m5nr$accession$name
     [1] "accession"
    
     $m5nr$accession$description
     [1] "Return annotation of given source protein ID"
    
     $m5nr$accession$parameters
     $m5nr$accession$parameters$body
     named list()
    
     $m5nr$accession$parameters$required
     $m5nr$accession$parameters$required$id
     [1] "string" "unique identifier from source DB"
    
    
     $m5nr$accession$parameters$options
     $m5nr$accession$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$accession$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$accession$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$accession$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $m5nr$accession$method
     [1] "GET"
    
     $m5nr$accession$type
     [1] "synchronous"
    
     $m5nr$accession$attributes
     $m5nr$accession$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$accession$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$accession$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$accession$attributes$data
     $m5nr$accession$attributes$data[[1]]
     [1] "list"
    
     $m5nr$accession$attributes$data[[2]]
     $m5nr$accession$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$accession$attributes$data[[2]][[2]]
     $m5nr$accession$attributes$data[[2]][[2]][[1]]
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$accession$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$accession$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$accession$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$accession$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$accession$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$accession$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $m5nr$alias
     $m5nr$alias$request
     [1] "http://api.metagenomics.anl.gov/m5nr/alias/{text}"
    
     $m5nr$alias$example
     [1] "http://api.metagenomics.anl.gov/m5nr/alias/IPR001478"
     [2] "retrieve M5NR data for db_xref ID 'IPR001478'"
    
     $m5nr$alias$name
     [1] "alias"
    
     $m5nr$alias$description
     [1] "Return annotations for alias IDs containing the given text"
    
     $m5nr$alias$parameters
     $m5nr$alias$parameters$body
     named list()
    
     $m5nr$alias$parameters$required
     $m5nr$alias$parameters$required$text
     [1] "string" "text string of partial alias"
    
    
     $m5nr$alias$parameters$options
     $m5nr$alias$parameters$options$source
     [1] "string" "source name to restrict search by"
    
     $m5nr$alias$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$alias$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$alias$parameters$options$exact
     [1] "boolean"
     [2] "if true return only those annotations that exactly match input text, default is false"
    
     $m5nr$alias$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$alias$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $m5nr$alias$method
     [1] "GET"
    
     $m5nr$alias$type
     [1] "synchronous"
    
     $m5nr$alias$attributes
     $m5nr$alias$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$alias$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$alias$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$alias$attributes$data
     $m5nr$alias$attributes$data[[1]]
     [1] "list"
    
     $m5nr$alias$attributes$data[[2]]
     $m5nr$alias$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$alias$attributes$data[[2]][[2]]
     $m5nr$alias$attributes$data[[2]][[2]][[1]]
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$alias$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$alias$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$alias$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$alias$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$alias$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$alias$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $m5nr$md5
     $m5nr$md5$request
     [1] "http://api.metagenomics.anl.gov/m5nr/md5/{id}"
    
     $m5nr$md5$example
     [1] "http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro"
     [2] "retrieve InterPro M5NR data for md5sum '000821a2e2f63df1a3873e4b280002a8'"
    
     $m5nr$md5$name
     [1] "md5"
    
     $m5nr$md5$description
     [1] "Return annotation(s) or sequence of given md5sum (M5NR ID)"
    
     $m5nr$md5$parameters
     $m5nr$md5$parameters$body
     named list()
    
     $m5nr$md5$parameters$required
     $m5nr$md5$parameters$required$id
     [1] "string"
     [2] "unique identifier in form of md5 checksum"
    
    
     $m5nr$md5$parameters$options
     $m5nr$md5$parameters$options$source
     [1] "string" "source name to restrict search by"
    
     $m5nr$md5$parameters$options$format
     $m5nr$md5$parameters$options$format[[1]]
     [1] "cv"
    
     $m5nr$md5$parameters$options$format[[2]]
     $m5nr$md5$parameters$options$format[[2]][[1]]
     [1] "fasta" "return sequences in fasta format"
    
     $m5nr$md5$parameters$options$format[[2]][[2]]
     [1] "json" "return sequences in json struct"
    
    
    
     $m5nr$md5$parameters$options$sequence
     [1] "boolean"
     [2] "if true return sequence output, else return annotation output, default is false"
    
     $m5nr$md5$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$md5$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$md5$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$md5$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $m5nr$md5$method
     [1] "GET"
    
     $m5nr$md5$type
     [1] "synchronous"
    
     $m5nr$md5$attributes
     $m5nr$md5$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$md5$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$md5$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$md5$attributes$data
     $m5nr$md5$attributes$data[[1]]
     [1] "list"
    
     $m5nr$md5$attributes$data[[2]]
     $m5nr$md5$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$md5$attributes$data[[2]][[2]]
     $m5nr$md5$attributes$data[[2]][[2]][[1]]
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$md5$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$md5$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$md5$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$md5$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$md5$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$md5$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $m5nr$`function`
     $m5nr$`function`$request
     [1] "http://api.metagenomics.anl.gov/m5nr/function/{text}"
    
     $m5nr$`function`$example
     [1] "http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank"
     [2] "retrieve GenBank M5NR data for function names containing string 'sulfatase'"
    
     $m5nr$`function`$name
     [1] "function"
    
     $m5nr$`function`$description
     [1] "Return annotations for function names containing the given text"
    
     $m5nr$`function`$parameters
     $m5nr$`function`$parameters$body
     named list()
    
     $m5nr$`function`$parameters$required
     $m5nr$`function`$parameters$required$text
     [1] "string"
     [2] "text string of partial function name"
    
    
     $m5nr$`function`$parameters$options
     $m5nr$`function`$parameters$options$source
     [1] "string" "source name to restrict search by"
    
     $m5nr$`function`$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$`function`$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$`function`$parameters$options$exact
     [1] "boolean"
     [2] "if true return only those annotations that exactly match input text, default is false"
    
     $m5nr$`function`$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$`function`$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
     $m5nr$`function`$parameters$options$inverse
     [1] "boolean"
     [2] "if true return only those annotations that do not match input text, default is false"
    
    
    
     $m5nr$`function`$method
     [1] "GET"
    
     $m5nr$`function`$type
     [1] "synchronous"
    
     $m5nr$`function`$attributes
     $m5nr$`function`$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$`function`$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$`function`$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$`function`$attributes$data
     $m5nr$`function`$attributes$data[[1]]
     [1] "list"
    
     $m5nr$`function`$attributes$data[[2]]
     $m5nr$`function`$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$`function`$attributes$data[[2]][[2]]
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$`function`$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$`function`$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$`function`$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$`function`$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$`function`$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$`function`$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $m5nr$organism
     $m5nr$organism$request
     [1] "http://api.metagenomics.anl.gov/m5nr/organism/{text}"
    
     $m5nr$organism$example
     [1] "http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG"
     [2] "retrieve KEGG M5NR data for organism names containing string 'akkermansia'"
    
     $m5nr$organism$name
     [1] "organism"
    
     $m5nr$organism$description
     [1] "Return annotations for organism names containing the given text"
    
     $m5nr$organism$parameters
     $m5nr$organism$parameters$body
     named list()
    
     $m5nr$organism$parameters$required
     $m5nr$organism$parameters$required$text
     [1] "string"
     [2] "text string of partial organism name"
    
    
     $m5nr$organism$parameters$options
     $m5nr$organism$parameters$options$source
     [1] "string" "source name to restrict search by"
    
     $m5nr$organism$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$organism$parameters$options$exact
     [1] "boolean"
     [2] "if true return only those annotations that exactly match input text, default is false"
    
     $m5nr$organism$parameters$options$inverse
     [1] "boolean"
     [2] "if true return only those annotations that do not match input text, default is false"
    
     $m5nr$organism$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$organism$parameters$options$tax_level
     $m5nr$organism$parameters$options$tax_level[[1]]
     [1] "cv"
    
     $m5nr$organism$parameters$options$tax_level[[2]]
     $m5nr$organism$parameters$options$tax_level[[2]][[1]]
     [1] "strain" "bottom organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[2]]
     [1] "species" "organism type level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[3]]
     [1] "genus" "organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[4]]
     [1] "family" "organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[5]]
     [1] "order" "organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[6]]
     [1] "class" "organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[7]]
     [1] "phylum" "organism taxanomic level"
    
     $m5nr$organism$parameters$options$tax_level[[2]][[8]]
     [1] "domain" "top organism taxanomic level"
    
    
    
     $m5nr$organism$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$organism$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $m5nr$organism$method
     [1] "GET"
    
     $m5nr$organism$type
     [1] "synchronous"
    
     $m5nr$organism$attributes
     $m5nr$organism$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$organism$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$organism$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$organism$attributes$data
     $m5nr$organism$attributes$data[[1]]
     [1] "list"
    
     $m5nr$organism$attributes$data[[2]]
     $m5nr$organism$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$organism$attributes$data[[2]][[2]]
     $m5nr$organism$attributes$data[[2]][[2]][[1]]
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$organism$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$organism$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$organism$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$organism$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$organism$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$organism$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $m5nr$sequence
     $m5nr$sequence$request
     [1] "http://api.metagenomics.anl.gov/m5nr/sequence/{text}"
    
     $m5nr$sequence$example
     [1] "http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL"
     [2] "retrieve TrEMBL M5NR data for md5sum of sequence 'MAGENHQWQGSIL'"
    
     $m5nr$sequence$name
     [1] "sequence"
    
     $m5nr$sequence$description
     [1] "Return annotation(s) for md5sum (M5NR ID) of given sequence"
    
     $m5nr$sequence$parameters
     $m5nr$sequence$parameters$body
     named list()
    
     $m5nr$sequence$parameters$required
     $m5nr$sequence$parameters$required$text
     [1] "string" "text string of protein sequence"
    
    
     $m5nr$sequence$parameters$options
     $m5nr$sequence$parameters$options$source
     [1] "string" "source name to restrict search by"
    
     $m5nr$sequence$parameters$options$version
     [1] "integer" "M5NR version, default 10"
    
     $m5nr$sequence$parameters$options$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $m5nr$sequence$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $m5nr$sequence$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $m5nr$sequence$method
     [1] "GET"
    
     $m5nr$sequence$type
     [1] "synchronous"
    
     $m5nr$sequence$attributes
     $m5nr$sequence$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $m5nr$sequence$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $m5nr$sequence$attributes$version
     [1] "integer" "version of M5NR"
    
     $m5nr$sequence$attributes$data
     $m5nr$sequence$attributes$data[[1]]
     [1] "list"
    
     $m5nr$sequence$attributes$data[[2]]
     $m5nr$sequence$attributes$data[[2]][[1]]
     [1] "object"
    
     $m5nr$sequence$attributes$data[[2]][[2]]
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$source
     [1] "string" "source name"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$`function`
     [1] "string" "function annotation"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$type
     [1] "string" "source type"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$ncbi_tax_id
     [1] "int" "organism ncbi tax_id"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$organism
     [1] "string" "organism annotation"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$md5
     [1] "string" "md5 checksum - M5NR ID"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias[[1]]
     [1] "list"
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$alias[[2]]
     [1] "string" "db_xref alaises"
    
    
     $m5nr$sequence$attributes$data[[2]][[2]][[1]]$accession
     [1] "string" "unique identifier given by source"
    
    
     $m5nr$sequence$attributes$data[[2]][[2]][[2]]
     [1] "annotation object"
    
    
    
    
     $m5nr$sequence$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $m5nr$sequence$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $m5nr$sequence$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $m5nr$sequence$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
    
     $matrix
     $matrix$info
     $matrix$info$parameters
     $matrix$info$parameters$body
     named list()
    
     $matrix$info$parameters$required
     named list()
    
     $matrix$info$parameters$options
     named list()
    
    
     $matrix$info$request
     [1] "http://api.metagenomics.anl.gov/matrix"
    
     $matrix$info$name
     [1] "info"
    
     $matrix$info$type
     [1] "synchronous"
    
     $matrix$info$method
     [1] "GET"
    
     $matrix$info$attributes
     [1] "self"
    
     $matrix$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $matrix$organism
     $matrix$organism$request
     [1] "http://api.metagenomics.anl.gov/matrix/organism"
    
     $matrix$organism$example
     [1] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15"
     [2] "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
    
     $matrix$organism$name
     [1] "organism"
    
     $matrix$organism$description
     [1] "Returns a BIOM object."
    
     $matrix$organism$parameters
     $matrix$organism$parameters$body
     named list()
    
     $matrix$organism$parameters$required
     named list()
    
     $matrix$organism$parameters$options
     $matrix$organism$parameters$options$asynchronous
     [1] "boolean"
     [2] "if true return process id to query status resource for results, default is false"
    
     $matrix$organism$parameters$options$source
     $matrix$organism$parameters$options$source[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$source[[2]]
     $matrix$organism$parameters$options$source[[2]][[1]]
     [1] "M5NR" "comprehensive protein database"
    
     $matrix$organism$parameters$options$source[[2]][[2]]
     [1] "M5RNA" "comprehensive RNA database"
    
     $matrix$organism$parameters$options$source[[2]][[3]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[4]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[5]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[6]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[7]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[8]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[9]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[10]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[11]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[12]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[13]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$organism$parameters$options$source[[2]][[14]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
    
    
     $matrix$organism$parameters$options$result_type
     $matrix$organism$parameters$options$result_type[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$result_type[[2]]
     $matrix$organism$parameters$options$result_type[[2]][[1]]
     [1] "abundance"
     [2] "number of reads with hits in annotation"
    
     $matrix$organism$parameters$options$result_type[[2]][[2]]
     [1] "evalue"
     [2] "average e-value exponent of hits in annotation"
    
     $matrix$organism$parameters$options$result_type[[2]][[3]]
     [1] "identity"
     [2] "average percent identity of hits in annotation"
    
     $matrix$organism$parameters$options$result_type[[2]][[4]]
     [1] "length"
     [2] "average alignment length of hits in annotation"
    
    
    
     $matrix$organism$parameters$options$filter
     [1] "string"
     [2] "filter the return results to only include abundances based on genes with this function"
    
     $matrix$organism$parameters$options$group_level
     $matrix$organism$parameters$options$group_level[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$group_level[[2]]
     $matrix$organism$parameters$options$group_level[[2]][[1]]
     [1] "strain" "bottom organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[2]]
     [1] "species" "organism type level"
    
     $matrix$organism$parameters$options$group_level[[2]][[3]]
     [1] "genus" "organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[4]]
     [1] "family" "organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[5]]
     [1] "order" "organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[6]]
     [1] "class" "organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[7]]
     [1] "phylum" "organism taxanomic level"
    
     $matrix$organism$parameters$options$group_level[[2]][[8]]
     [1] "domain" "top organism taxanomic level"
    
    
    
     $matrix$organism$parameters$options$taxid
     [1] "boolean"
     [2] "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
    
     $matrix$organism$parameters$options$grep
     [1] "string"
     [2] "filter the return results to only include annotations that contain this text"
    
     $matrix$organism$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $matrix$organism$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $matrix$organism$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $matrix$organism$parameters$options$filter_source
     $matrix$organism$parameters$options$filter_source[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$filter_source[[2]]
     $matrix$organism$parameters$options$filter_source[[2]][[1]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $matrix$organism$parameters$options$filter_source[[2]][[2]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $matrix$organism$parameters$options$filter_source[[2]][[3]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $matrix$organism$parameters$options$filter_source[[2]][[4]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $matrix$organism$parameters$options$hide_metadata
     [1] "boolean"
     [2] "if true do not return metagenome metadata in 'columns' object, default is false"
    
     $matrix$organism$parameters$options$id
     [1] "string"
     [2] "one or more metagenome or project unique identifier"
    
     $matrix$organism$parameters$options$filter_level
     $matrix$organism$parameters$options$filter_level[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$filter_level[[2]]
     $matrix$organism$parameters$options$filter_level[[2]][[1]]
     [1] "function" "bottom function ontology level"
    
     $matrix$organism$parameters$options$filter_level[[2]][[2]]
     [1] "level3" "function ontology level"
    
     $matrix$organism$parameters$options$filter_level[[2]][[3]]
     [1] "level2" "function ontology level"
    
     $matrix$organism$parameters$options$filter_level[[2]][[4]]
     [1] "level1" "top function ontology level"
    
    
    
     $matrix$organism$parameters$options$hit_type
     $matrix$organism$parameters$options$hit_type[[1]]
     [1] "cv"
    
     $matrix$organism$parameters$options$hit_type[[2]]
     $matrix$organism$parameters$options$hit_type[[2]][[1]]
     [1] "all"
     [2] "returns results based on all organisms that map to top hit per read-feature"
    
     $matrix$organism$parameters$options$hit_type[[2]][[2]]
     [1] "single"
     [2] "returns results based on a single organism for top hit per read-feature"
    
     $matrix$organism$parameters$options$hit_type[[2]][[3]]
     [1] "lca"
     [2] "returns results based on the Least Common Ancestor for all organisms (M5NR+M5RNA only) that map to hits from a read-feature"
    
    
    
    
    
     $matrix$organism$method
     [1] "GET"
    
     $matrix$organism$type
     [1] "synchronous or asynchronous"
    
     $matrix$organism$attributes
     $matrix$organism$attributes$generated_by
     [1] "string" "identifier of the data generator"
    
     $matrix$organism$attributes$matrix_type
     [1] "string"
     [2] "type of the data encoding matrix (dense or sparse)"
    
     $matrix$organism$attributes$date
     [1] "date" "time the output data was generated"
    
     $matrix$organism$attributes$data
     $matrix$organism$attributes$data[[1]]
     [1] "list"
    
     $matrix$organism$attributes$data[[2]]
     $matrix$organism$attributes$data[[2]][[1]]
     [1] "list"
    
     $matrix$organism$attributes$data[[2]][[2]]
     [1] "float" "the matrix values"
    
    
    
     $matrix$organism$attributes$rows
     $matrix$organism$attributes$rows[[1]]
     [1] "list"
    
     $matrix$organism$attributes$rows[[2]]
     $matrix$organism$attributes$rows[[2]][[1]]
     [1] "object"
    
     $matrix$organism$attributes$rows[[2]][[2]]
     $matrix$organism$attributes$rows[[2]][[2]][[1]]
     $matrix$organism$attributes$rows[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$organism$attributes$rows[[2]][[2]][[1]]$id
     [1] "string" "unique annotation text"
    
    
     $matrix$organism$attributes$rows[[2]][[2]][[2]]
     [1] "rows object"
    
    
    
    
     $matrix$organism$attributes$matrix_element_value
     [1] "string"
     [2] "result_type of the elements in the return matrix"
    
     $matrix$organism$attributes$matrix_element_type
     [1] "string"
     [2] "data type of the elements in the return matrix"
    
     $matrix$organism$attributes$format_url
     [1] "string" "url to the format specification"
    
     $matrix$organism$attributes$format
     [1] "string" "format specification name"
    
     $matrix$organism$attributes$columns
     $matrix$organism$attributes$columns[[1]]
     [1] "list"
    
     $matrix$organism$attributes$columns[[2]]
     $matrix$organism$attributes$columns[[2]][[1]]
     [1] "object"
    
     $matrix$organism$attributes$columns[[2]][[2]]
     $matrix$organism$attributes$columns[[2]][[2]][[1]]
     $matrix$organism$attributes$columns[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$organism$attributes$columns[[2]][[2]][[1]]$id
     [1] "string" "unique metagenome identifier"
    
    
     $matrix$organism$attributes$columns[[2]][[2]][[2]]
     [1] "columns object"
    
    
    
    
     $matrix$organism$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $matrix$organism$attributes$shape
     $matrix$organism$attributes$shape[[1]]
     [1] "list"
    
     $matrix$organism$attributes$shape[[2]]
     [1] "integer"
     [2] "list of the dimension sizes of the return matrix"
    
    
     $matrix$organism$attributes$id
     [1] "string" "unique object identifier"
    
     $matrix$organism$attributes$type
     [1] "string"
     [2] "type of the data in the return table (taxon, function or gene)"
    
    
    
     $matrix$`function`
     $matrix$`function`$request
     [1] "http://api.metagenomics.anl.gov/matrix/function"
    
     $matrix$`function`$example
     [1] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes"
     [2] "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtered to return annotations only in phylum Firmicutes"
    
     $matrix$`function`$name
     [1] "function"
    
     $matrix$`function`$description
     [1] "Returns a BIOM object."
    
     $matrix$`function`$parameters
     $matrix$`function`$parameters$body
     named list()
    
     $matrix$`function`$parameters$required
     named list()
    
     $matrix$`function`$parameters$options
     $matrix$`function`$parameters$options$asynchronous
     [1] "boolean"
     [2] "if true return process id to query status resource for results, default is false"
    
     $matrix$`function`$parameters$options$source
     $matrix$`function`$parameters$options$source[[1]]
     [1] "cv"
    
     $matrix$`function`$parameters$options$source[[2]]
     $matrix$`function`$parameters$options$source[[2]][[1]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $matrix$`function`$parameters$options$source[[2]][[2]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $matrix$`function`$parameters$options$source[[2]][[3]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $matrix$`function`$parameters$options$source[[2]][[4]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $matrix$`function`$parameters$options$result_type
     $matrix$`function`$parameters$options$result_type[[1]]
     [1] "cv"
    
     $matrix$`function`$parameters$options$result_type[[2]]
     $matrix$`function`$parameters$options$result_type[[2]][[1]]
     [1] "abundance"
     [2] "number of reads with hits in annotation"
    
     $matrix$`function`$parameters$options$result_type[[2]][[2]]
     [1] "evalue"
     [2] "average e-value exponent of hits in annotation"
    
     $matrix$`function`$parameters$options$result_type[[2]][[3]]
     [1] "identity"
     [2] "average percent identity of hits in annotation"
    
     $matrix$`function`$parameters$options$result_type[[2]][[4]]
     [1] "length"
     [2] "average alignment length of hits in annotation"
    
    
    
     $matrix$`function`$parameters$options$filter
     [1] "string"
     [2] "filter the return results to only include abundances based on genes with this organism"
    
     $matrix$`function`$parameters$options$group_level
     $matrix$`function`$parameters$options$group_level[[1]]
     [1] "cv"
    
     $matrix$`function`$parameters$options$group_level[[2]]
     $matrix$`function`$parameters$options$group_level[[2]][[1]]
     [1] "function" "bottom function ontology level"
    
     $matrix$`function`$parameters$options$group_level[[2]][[2]]
     [1] "level3" "function ontology level"
    
     $matrix$`function`$parameters$options$group_level[[2]][[3]]
     [1] "level2" "function ontology level"
    
     $matrix$`function`$parameters$options$group_level[[2]][[4]]
     [1] "level1" "top function ontology level"
    
    
    
     $matrix$`function`$parameters$options$grep
     [1] "string"
     [2] "filter the return results to only include annotations that contain this text"
    
     $matrix$`function`$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $matrix$`function`$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $matrix$`function`$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $matrix$`function`$parameters$options$filter_source
     $matrix$`function`$parameters$options$filter_source[[1]]
     [1] "cv"
    
     $matrix$`function`$parameters$options$filter_source[[2]]
     $matrix$`function`$parameters$options$filter_source[[2]][[1]]
     [1] "M5NR" "comprehensive protein database"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[2]]
     [1] "M5RNA" "comprehensive RNA database"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[3]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[4]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[5]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[6]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[7]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[8]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[9]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[10]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[11]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[12]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[13]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$`function`$parameters$options$filter_source[[2]][[14]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
    
    
     $matrix$`function`$parameters$options$hide_metadata
     [1] "boolean"
     [2] "if true do not return metagenome metadata in 'columns' object, default is false"
    
     $matrix$`function`$parameters$options$id
     [1] "string"
     [2] "one or more metagenome or project unique identifier"
    
     $matrix$`function`$parameters$options$filter_level
     $matrix$`function`$parameters$options$filter_level[[1]]
     [1] "cv"
    
     $matrix$`function`$parameters$options$filter_level[[2]]
     $matrix$`function`$parameters$options$filter_level[[2]][[1]]
     [1] "strain" "bottom organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[2]]
     [1] "species" "organism type level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[3]]
     [1] "genus" "organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[4]]
     [1] "family" "organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[5]]
     [1] "order" "organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[6]]
     [1] "class" "organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[7]]
     [1] "phylum" "organism taxanomic level"
    
     $matrix$`function`$parameters$options$filter_level[[2]][[8]]
     [1] "domain" "top organism taxanomic level"
    
    
    
    
    
     $matrix$`function`$method
     [1] "GET"
    
     $matrix$`function`$type
     [1] "synchronous or asynchronous"
    
     $matrix$`function`$attributes
     $matrix$`function`$attributes$generated_by
     [1] "string" "identifier of the data generator"
    
     $matrix$`function`$attributes$matrix_type
     [1] "string"
     [2] "type of the data encoding matrix (dense or sparse)"
    
     $matrix$`function`$attributes$date
     [1] "date" "time the output data was generated"
    
     $matrix$`function`$attributes$data
     $matrix$`function`$attributes$data[[1]]
     [1] "list"
    
     $matrix$`function`$attributes$data[[2]]
     $matrix$`function`$attributes$data[[2]][[1]]
     [1] "list"
    
     $matrix$`function`$attributes$data[[2]][[2]]
     [1] "float" "the matrix values"
    
    
    
     $matrix$`function`$attributes$rows
     $matrix$`function`$attributes$rows[[1]]
     [1] "list"
    
     $matrix$`function`$attributes$rows[[2]]
     $matrix$`function`$attributes$rows[[2]][[1]]
     [1] "object"
    
     $matrix$`function`$attributes$rows[[2]][[2]]
     $matrix$`function`$attributes$rows[[2]][[2]][[1]]
     $matrix$`function`$attributes$rows[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$`function`$attributes$rows[[2]][[2]][[1]]$id
     [1] "string" "unique annotation text"
    
    
     $matrix$`function`$attributes$rows[[2]][[2]][[2]]
     [1] "rows object"
    
    
    
    
     $matrix$`function`$attributes$matrix_element_value
     [1] "string"
     [2] "result_type of the elements in the return matrix"
    
     $matrix$`function`$attributes$matrix_element_type
     [1] "string"
     [2] "data type of the elements in the return matrix"
    
     $matrix$`function`$attributes$format_url
     [1] "string" "url to the format specification"
    
     $matrix$`function`$attributes$format
     [1] "string" "format specification name"
    
     $matrix$`function`$attributes$columns
     $matrix$`function`$attributes$columns[[1]]
     [1] "list"
    
     $matrix$`function`$attributes$columns[[2]]
     $matrix$`function`$attributes$columns[[2]][[1]]
     [1] "object"
    
     $matrix$`function`$attributes$columns[[2]][[2]]
     $matrix$`function`$attributes$columns[[2]][[2]][[1]]
     $matrix$`function`$attributes$columns[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$`function`$attributes$columns[[2]][[2]][[1]]$id
     [1] "string" "unique metagenome identifier"
    
    
     $matrix$`function`$attributes$columns[[2]][[2]][[2]]
     [1] "columns object"
    
    
    
    
     $matrix$`function`$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $matrix$`function`$attributes$shape
     $matrix$`function`$attributes$shape[[1]]
     [1] "list"
    
     $matrix$`function`$attributes$shape[[2]]
     [1] "integer"
     [2] "list of the dimension sizes of the return matrix"
    
    
     $matrix$`function`$attributes$id
     [1] "string" "unique object identifier"
    
     $matrix$`function`$attributes$type
     [1] "string"
     [2] "type of the data in the return table (taxon, function or gene)"
    
    
    
     $matrix$feature
     $matrix$feature$request
     [1] "http://api.metagenomics.anl.gov/matrix/feature"
    
     $matrix$feature$example
     [1] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25"
     [2] "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
    
     $matrix$feature$name
     [1] "feature"
    
     $matrix$feature$description
     [1] "Returns a BIOM object."
    
     $matrix$feature$parameters
     $matrix$feature$parameters$body
     named list()
    
     $matrix$feature$parameters$required
     named list()
    
     $matrix$feature$parameters$options
     $matrix$feature$parameters$options$asynchronous
     [1] "boolean"
     [2] "if true return process id to query status resource for results, default is false"
    
     $matrix$feature$parameters$options$source
     $matrix$feature$parameters$options$source[[1]]
     [1] "cv"
    
     $matrix$feature$parameters$options$source[[2]]
     $matrix$feature$parameters$options$source[[2]][[1]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[2]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[3]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[4]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[5]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[6]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[7]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[8]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[9]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[10]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[11]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $matrix$feature$parameters$options$source[[2]][[12]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
    
    
     $matrix$feature$parameters$options$result_type
     $matrix$feature$parameters$options$result_type[[1]]
     [1] "cv"
    
     $matrix$feature$parameters$options$result_type[[2]]
     $matrix$feature$parameters$options$result_type[[2]][[1]]
     [1] "abundance"
     [2] "number of reads with hits in annotation"
    
     $matrix$feature$parameters$options$result_type[[2]][[2]]
     [1] "evalue"
     [2] "average e-value exponent of hits in annotation"
    
     $matrix$feature$parameters$options$result_type[[2]][[3]]
     [1] "identity"
     [2] "average percent identity of hits in annotation"
    
     $matrix$feature$parameters$options$result_type[[2]][[4]]
     [1] "length"
     [2] "average alignment length of hits in annotation"
    
    
    
     $matrix$feature$parameters$options$filter
     [1] "string"
     [2] "filter the return results to only include abundances based on genes with this organism"
    
     $matrix$feature$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $matrix$feature$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $matrix$feature$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $matrix$feature$parameters$options$hide_annotation
     [1] "boolean"
     [2] "if true do not return feature metadata in 'rows' object, default is false"
    
     $matrix$feature$parameters$options$id
     [1] "string"
     [2] "one or more metagenome or project unique identifier"
    
     $matrix$feature$parameters$options$hide_metadata
     [1] "boolean"
     [2] "if true do not return metagenome metadata in 'columns' object, default is false"
    
     $matrix$feature$parameters$options$filter_level
     $matrix$feature$parameters$options$filter_level[[1]]
     [1] "cv"
    
     $matrix$feature$parameters$options$filter_level[[2]]
     $matrix$feature$parameters$options$filter_level[[2]][[1]]
     [1] "strain" "bottom organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[2]]
     [1] "species" "organism type level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[3]]
     [1] "genus" "organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[4]]
     [1] "family" "organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[5]]
     [1] "order" "organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[6]]
     [1] "class" "organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[7]]
     [1] "phylum" "organism taxanomic level"
    
     $matrix$feature$parameters$options$filter_level[[2]][[8]]
     [1] "domain" "top organism taxanomic level"
    
    
    
    
    
     $matrix$feature$method
     [1] "GET"
    
     $matrix$feature$type
     [1] "synchronous or asynchronous"
    
     $matrix$feature$attributes
     $matrix$feature$attributes$generated_by
     [1] "string" "identifier of the data generator"
    
     $matrix$feature$attributes$matrix_type
     [1] "string"
     [2] "type of the data encoding matrix (dense or sparse)"
    
     $matrix$feature$attributes$date
     [1] "date" "time the output data was generated"
    
     $matrix$feature$attributes$data
     $matrix$feature$attributes$data[[1]]
     [1] "list"
    
     $matrix$feature$attributes$data[[2]]
     $matrix$feature$attributes$data[[2]][[1]]
     [1] "list"
    
     $matrix$feature$attributes$data[[2]][[2]]
     [1] "float" "the matrix values"
    
    
    
     $matrix$feature$attributes$rows
     $matrix$feature$attributes$rows[[1]]
     [1] "list"
    
     $matrix$feature$attributes$rows[[2]]
     $matrix$feature$attributes$rows[[2]][[1]]
     [1] "object"
    
     $matrix$feature$attributes$rows[[2]][[2]]
     $matrix$feature$attributes$rows[[2]][[2]][[1]]
     $matrix$feature$attributes$rows[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$feature$attributes$rows[[2]][[2]][[1]]$id
     [1] "string" "unique annotation text"
    
    
     $matrix$feature$attributes$rows[[2]][[2]][[2]]
     [1] "rows object"
    
    
    
    
     $matrix$feature$attributes$matrix_element_value
     [1] "string"
     [2] "result_type of the elements in the return matrix"
    
     $matrix$feature$attributes$matrix_element_type
     [1] "string"
     [2] "data type of the elements in the return matrix"
    
     $matrix$feature$attributes$format_url
     [1] "string" "url to the format specification"
    
     $matrix$feature$attributes$format
     [1] "string" "format specification name"
    
     $matrix$feature$attributes$columns
     $matrix$feature$attributes$columns[[1]]
     [1] "list"
    
     $matrix$feature$attributes$columns[[2]]
     $matrix$feature$attributes$columns[[2]][[1]]
     [1] "object"
    
     $matrix$feature$attributes$columns[[2]][[2]]
     $matrix$feature$attributes$columns[[2]][[2]][[1]]
     $matrix$feature$attributes$columns[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $matrix$feature$attributes$columns[[2]][[2]][[1]]$id
     [1] "string" "unique metagenome identifier"
    
    
     $matrix$feature$attributes$columns[[2]][[2]][[2]]
     [1] "columns object"
    
    
    
    
     $matrix$feature$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $matrix$feature$attributes$shape
     $matrix$feature$attributes$shape[[1]]
     [1] "list"
    
     $matrix$feature$attributes$shape[[2]]
     [1] "integer"
     [2] "list of the dimension sizes of the return matrix"
    
    
     $matrix$feature$attributes$id
     [1] "string" "unique object identifier"
    
     $matrix$feature$attributes$type
     [1] "string"
     [2] "type of the data in the return table (taxon, function or gene)"
    
    
    
    
     $metadata
     $metadata$info
     $metadata$info$parameters
     $metadata$info$parameters$body
     named list()
    
     $metadata$info$parameters$required
     named list()
    
     $metadata$info$parameters$options
     named list()
    
    
     $metadata$info$request
     [1] "http://api.metagenomics.anl.gov/metadata"
    
     $metadata$info$name
     [1] "info"
    
     $metadata$info$type
     [1] "synchronous"
    
     $metadata$info$method
     [1] "GET"
    
     $metadata$info$attributes
     [1] "self"
    
     $metadata$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $metadata$template
     $metadata$template$request
     [1] "http://api.metagenomics.anl.gov/metadata/template"
    
     $metadata$template$example
     [1] "http://api.metagenomics.anl.gov/metadata/template"
     [2] "metadata template"
    
     $metadata$template$name
     [1] "template"
    
     $metadata$template$description
     [1] "Returns static template for metadata object relationships and types"
    
     $metadata$template$parameters
     $metadata$template$parameters$body
     named list()
    
     $metadata$template$parameters$required
     named list()
    
     $metadata$template$parameters$options
     named list()
    
    
     $metadata$template$method
     [1] "GET"
    
     $metadata$template$type
     [1] "synchronous"
    
     $metadata$template$attributes
     $metadata$template$attributes$ep
     $metadata$template$attributes$ep[[1]]
     [1] "hash"
    
     $metadata$template$attributes$ep[[2]]
     $metadata$template$attributes$ep[[2]][[1]]
     $metadata$template$attributes$ep[[2]][[1]]$value
     [1] "hash" "hash of metadata objects by label"
    
     $metadata$template$attributes$ep[[2]][[1]]$key
     [1] "string" "enviromental package type"
    
    
     $metadata$template$attributes$ep[[2]][[2]]
     [1] "eps and their metadata"
    
    
    
     $metadata$template$attributes$project
     $metadata$template$attributes$project[[1]]
     [1] "hash"
    
     $metadata$template$attributes$project[[2]]
     $metadata$template$attributes$project[[2]][[1]]
     $metadata$template$attributes$project[[2]][[1]]$value
     [1] "hash" "hash of metadata objects by label"
    
     $metadata$template$attributes$project[[2]][[1]]$key
     [1] "string" "project type"
    
    
     $metadata$template$attributes$project[[2]][[2]]
     [1] "projects and their metadata"
    
    
    
     $metadata$template$attributes$library
     $metadata$template$attributes$library[[1]]
     [1] "hash"
    
     $metadata$template$attributes$library[[2]]
     $metadata$template$attributes$library[[2]][[1]]
     $metadata$template$attributes$library[[2]][[1]]$value
     [1] "hash" "hash of metadata objects by label"
    
     $metadata$template$attributes$library[[2]][[1]]$key
     [1] "string" "library type"
    
    
     $metadata$template$attributes$library[[2]][[2]]
     [1] "libraries and their metadata"
    
    
    
     $metadata$template$attributes$sample
     $metadata$template$attributes$sample[[1]]
     [1] "hash"
    
     $metadata$template$attributes$sample[[2]]
     $metadata$template$attributes$sample[[2]][[1]]
     $metadata$template$attributes$sample[[2]][[1]]$value
     [1] "hash" "hash of metadata objects by label"
    
     $metadata$template$attributes$sample[[2]][[1]]$key
     [1] "string" "sample type"
    
    
     $metadata$template$attributes$sample[[2]][[2]]
     [1] "samples and their metadata"
    
    
    
    
    
     $metadata$cv
     $metadata$cv$request
     [1] "http://api.metagenomics.anl.gov/metadata/cv"
    
     $metadata$cv$example
     [1] "http://api.metagenomics.anl.gov/metadata/cv?label=country"
     [2] "metadata controlled vocabularies"
    
     $metadata$cv$name
     [1] "cv"
    
     $metadata$cv$description
     [1] "Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label and version options used, returns those specific values."
    
     $metadata$cv$parameters
     $metadata$cv$parameters$body
     named list()
    
     $metadata$cv$parameters$options
     $metadata$cv$parameters$options$version
     [1] "string"
     [2] "version of CV select list or ontology to use"
    
     $metadata$cv$parameters$options$label
     [1] "string" "metadata label"
    
    
     $metadata$cv$parameters$required
     named list()
    
    
     $metadata$cv$method
     [1] "GET"
    
     $metadata$cv$type
     [1] "synchronous"
    
     $metadata$cv$attributes
     $metadata$cv$attributes$ontology
     $metadata$cv$attributes$ontology[[1]]
     [1] "hash"
    
     $metadata$cv$attributes$ontology[[2]]
     $metadata$cv$attributes$ontology[[2]][[1]]
     $metadata$cv$attributes$ontology[[2]][[1]]$value
     $metadata$cv$attributes$ontology[[2]][[1]]$value[[1]]
     [1] "list"
    
     $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]]
     $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]][[1]]
     [1] "list"
    
     $metadata$cv$attributes$ontology[[2]][[1]]$value[[2]][[2]]
     [1] "string" "ontology term and ID"
    
    
    
     $metadata$cv$attributes$ontology[[2]][[1]]$key
     [1] "string" "metadata label"
    
    
     $metadata$cv$attributes$ontology[[2]][[2]]
     [1] "list of CV terms for metadata"
    
    
    
     $metadata$cv$attributes$ont_info
     $metadata$cv$attributes$ont_info[[1]]
     [1] "hash"
    
     $metadata$cv$attributes$ont_info[[2]]
     $metadata$cv$attributes$ont_info[[2]][[1]]
     $metadata$cv$attributes$ont_info[[2]][[1]]$value
     $metadata$cv$attributes$ont_info[[2]][[1]]$value[[1]]
     [1] "list"
    
     $metadata$cv$attributes$ont_info[[2]][[1]]$value[[2]]
     [1] "string" "ontology url and ID"
    
    
     $metadata$cv$attributes$ont_info[[2]][[1]]$key
     [1] "string" "metadata label"
    
    
     $metadata$cv$attributes$ont_info[[2]][[2]]
     [1] "term IDs for metadata"
    
    
    
     $metadata$cv$attributes$select
     $metadata$cv$attributes$select[[1]]
     [1] "hash"
    
     $metadata$cv$attributes$select[[2]]
     $metadata$cv$attributes$select[[2]][[1]]
     $metadata$cv$attributes$select[[2]][[1]]$value
     $metadata$cv$attributes$select[[2]][[1]]$value[[1]]
     [1] "list"
    
     $metadata$cv$attributes$select[[2]][[1]]$value[[2]]
     [1] "string" "CV term"
    
    
     $metadata$cv$attributes$select[[2]][[1]]$key
     [1] "string" "metadata label"
    
    
     $metadata$cv$attributes$select[[2]][[2]]
     [1] "list of CV terms for metadata"
    
    
    
    
    
     $metadata$ontology
     $metadata$ontology$request
     [1] "http://api.metagenomics.anl.gov/metadata/ontology"
    
     $metadata$ontology$example
     [1] "http://api.metagenomics.anl.gov/metadata/ontology?name=biome&version=2013-04-27"
     [2] "metadata ontology lookup"
    
     $metadata$ontology$name
     [1] "ontology"
    
     $metadata$ontology$description
     [1] "Returns static ontology used in metadata for the given name and version."
    
     $metadata$ontology$parameters
     $metadata$ontology$parameters$body
     named list()
    
     $metadata$ontology$parameters$options
     named list()
    
     $metadata$ontology$parameters$required
     $metadata$ontology$parameters$required$version
     [1] "string" "version of ontology to use"
    
     $metadata$ontology$parameters$required$name
     [1] "string" "ontology name"
    
    
    
     $metadata$ontology$method
     [1] "GET"
    
     $metadata$ontology$type
     [1] "synchronous"
    
     $metadata$ontology$attributes
     $metadata$ontology$attributes$version
     [1] "string" "version of this ontology"
    
     $metadata$ontology$attributes$rootNode
     [1] "string" "ontology ID of root"
    
     $metadata$ontology$attributes$name
     [1] "string" "ontology name"
    
     $metadata$ontology$attributes$type
     [1] "string" "this type"
    
     $metadata$ontology$attributes$showRoot
     [1] "boolean" "option to show root when displaying"
    
     $metadata$ontology$attributes$nodes
     $metadata$ontology$attributes$nodes[[1]]
     [1] "hash"
    
     $metadata$ontology$attributes$nodes[[2]]
     $metadata$ontology$attributes$nodes[[2]][[1]]
     $metadata$ontology$attributes$nodes[[2]][[1]]$value
     [1] "hash"
     [2] "hash of information and relationships for given ontology ID"
    
     $metadata$ontology$attributes$nodes[[2]][[1]]$key
     [1] "string" "ontology ID"
    
    
     $metadata$ontology$attributes$nodes[[2]][[2]]
     [1] "info for ontology ID"
    
    
    
    
    
     $metadata$export
     $metadata$export$request
     [1] "http://api.metagenomics.anl.gov/metadata/export/{ID}"
    
     $metadata$export$example
     [1] "http://api.metagenomics.anl.gov/metadata/export/mgp128"
     [2] "all metadata for project mgp128"
    
     $metadata$export$name
     [1] "export"
    
     $metadata$export$description
     [1] "Returns full nested metadata for a project in same format as template, or metadata for a single metagenome."
    
     $metadata$export$parameters
     $metadata$export$parameters$body
     named list()
    
     $metadata$export$parameters$required
     $metadata$export$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $metadata$export$parameters$options
     named list()
    
    
     $metadata$export$method
     [1] "GET"
    
     $metadata$export$type
     [1] "synchronous"
    
     $metadata$export$attributes
     $metadata$export$attributes$sampleNum
     [1] "int" "number of samples in project"
    
     $metadata$export$attributes$samples
     $metadata$export$attributes$samples[[1]]
     [1] "list"
    
     $metadata$export$attributes$samples[[2]]
     [1] "object"
     [2] "sample object containing sample metadata, sample libraries, sample envPackage"
    
    
     $metadata$export$attributes$name
     [1] "string" "human readable identifier"
    
     $metadata$export$attributes$data
     $metadata$export$attributes$data[[1]]
     [1] "hash"
    
     $metadata$export$attributes$data[[2]]
     $metadata$export$attributes$data[[2]][[1]]
     $metadata$export$attributes$data[[2]][[1]]$value
     [1] "object" "project metadata objects"
    
     $metadata$export$attributes$data[[2]][[1]]$key
     [1] "string" "metadata label"
    
    
     $metadata$export$attributes$data[[2]][[2]]
     [1] "hash of metadata by label"
    
    
    
     $metadata$export$attributes$id
     [1] "string" "unique object identifier"
    
    
    
     $metadata$validate
     $metadata$validate$request
     [1] "http://api.metagenomics.anl.gov/metadata/validate"
    
     $metadata$validate$example
     [1] "http://api.metagenomics.anl.gov/metadata/validate?category=sample&label=material&value=soil"
     [2] "check if 'soil' is a vaild term for sample material"
    
     $metadata$validate$name
     [1] "validate"
    
     $metadata$validate$description
     [1] "Validate given metadata value"
    
     $metadata$validate$parameters
     $metadata$validate$parameters$body
     named list()
    
     $metadata$validate$parameters$options
     $metadata$validate$parameters$options$group
     $metadata$validate$parameters$options$group[[1]]
     [1] "cv"
    
     $metadata$validate$parameters$options$group[[2]]
     $metadata$validate$parameters$options$group[[2]][[1]]
     [1] "mixs"
     [2] "label is part of MIxS (minimal) metadata"
    
     $metadata$validate$parameters$options$group[[2]][[2]]
     [1] "mims"
     [2] "label is part of MIMS (metagenome) metadata"
    
     $metadata$validate$parameters$options$group[[2]][[3]]
     [1] "migs"
     [2] "label is part of MIGS (genome) metadata"
    
    
    
     $metadata$validate$parameters$options$version
     [1] "string"
     [2] "version of CV select list or ontology to use"
    
     $metadata$validate$parameters$options$value
     [1] "string" "metadata value"
    
     $metadata$validate$parameters$options$label
     [1] "string" "metadata label"
    
     $metadata$validate$parameters$options$category
     $metadata$validate$parameters$options$category[[1]]
     [1] "cv"
    
     $metadata$validate$parameters$options$category[[2]]
     $metadata$validate$parameters$options$category[[2]][[1]]
     [1] "project" "label belongs to project metadata"
    
     $metadata$validate$parameters$options$category[[2]][[2]]
     [1] "sample" "label belongs to sample metadata"
    
     $metadata$validate$parameters$options$category[[2]][[3]]
     [1] "library" "label belongs to library metadata"
    
     $metadata$validate$parameters$options$category[[2]][[4]]
     [1] "env_package"
     [2] "label belongs to env_package metadata"
    
    
    
    
     $metadata$validate$parameters$required
     named list()
    
    
     $metadata$validate$method
     [1] "GET"
    
     $metadata$validate$type
     [1] "synchronous"
    
     $metadata$validate$attributes
     $metadata$validate$attributes$message
     [1] "string" "if not valid, reason why"
    
     $metadata$validate$attributes$is_valid
     [1] "boolean"
     [2] "the inputed value is valid for the given category and label"
    
    
    
    
     $metagenome
     $metagenome$info
     $metagenome$info$parameters
     $metagenome$info$parameters$body
     named list()
    
     $metagenome$info$parameters$required
     named list()
    
     $metagenome$info$parameters$options
     named list()
    
    
     $metagenome$info$request
     [1] "http://api.metagenomics.anl.gov/metagenome"
    
     $metagenome$info$name
     [1] "info"
    
     $metagenome$info$type
     [1] "synchronous"
    
     $metagenome$info$method
     [1] "GET"
    
     $metagenome$info$attributes
     [1] "self"
    
     $metagenome$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $metagenome$query
     $metagenome$query$request
     [1] "http://api.metagenomics.anl.gov/metagenome"
    
     $metagenome$query$example
     [1] "http://api.metagenomics.anl.gov/metagenome?limit=20&order=name"
     [2] "retrieve the first 20 metagenomes ordered by name"
    
     $metagenome$query$name
     [1] "query"
    
     $metagenome$query$description
     [1] "Returns a set of data matching the query criteria."
    
     $metagenome$query$parameters
     $metagenome$query$parameters$body
     named list()
    
     $metagenome$query$parameters$required
     named list()
    
     $metagenome$query$parameters$options
     $metagenome$query$parameters$options$verbosity
     $metagenome$query$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $metagenome$query$parameters$options$verbosity[[2]]
     $metagenome$query$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $metagenome$query$parameters$options$verbosity[[2]][[2]]
     [1] "mixs" "returns all GSC MIxS metadata"
    
     $metagenome$query$parameters$options$verbosity[[2]][[3]]
     [1] "metadata" "returns minimal with metadata"
    
     $metagenome$query$parameters$options$verbosity[[2]][[4]]
     [1] "stats" "returns minimal with statistics"
    
     $metagenome$query$parameters$options$verbosity[[2]][[5]]
     [1] "full" "returns all metadata and statistics"
    
    
    
     $metagenome$query$parameters$options$`function`
     [1] "string"
     [2] "search parameter: query string for function"
    
     $metagenome$query$parameters$options$status
     $metagenome$query$parameters$options$status[[1]]
     [1] "cv"
    
     $metagenome$query$parameters$options$status[[2]]
     $metagenome$query$parameters$options$status[[2]][[1]]
     [1] "both"
     [2] "returns all data (public and private) user has access to view"
    
     $metagenome$query$parameters$options$status[[2]][[2]]
     [1] "public" "returns all public data"
    
     $metagenome$query$parameters$options$status[[2]][[3]]
     [1] "private"
     [2] "returns private data user has access to view"
    
    
    
     $metagenome$query$parameters$options$match
     $metagenome$query$parameters$options$match[[1]]
     [1] "cv"
    
     $metagenome$query$parameters$options$match[[2]]
     $metagenome$query$parameters$options$match[[2]][[1]]
     [1] "all"
     [2] "return metagenomes that match all search parameters"
    
     $metagenome$query$parameters$options$match[[2]][[2]]
     [1] "any"
     [2] "return metagenomes that match any search parameters"
    
    
    
     $metagenome$query$parameters$options$direction
     $metagenome$query$parameters$options$direction[[1]]
     [1] "cv"
    
     $metagenome$query$parameters$options$direction[[2]]
     $metagenome$query$parameters$options$direction[[2]][[1]]
     [1] "asc" "sort by ascending order"
    
     $metagenome$query$parameters$options$direction[[2]][[2]]
     [1] "desc" "sort by descending order"
    
    
    
     $metagenome$query$parameters$options$order
     [1] "string"
     [2] "metagenome object field to sort by (default is id)"
    
     $metagenome$query$parameters$options$metadata
     [1] "string"
     [2] "search parameter: query string for any metadata field"
    
     $metagenome$query$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $metagenome$query$parameters$options$md5
     [1] "string"
     [2] "search parameter: md5 checksum of feature sequence"
    
     $metagenome$query$parameters$options$organism
     [1] "string"
     [2] "search parameter: query string for organism"
    
     $metagenome$query$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $metagenome$query$method
     [1] "GET"
    
     $metagenome$query$type
     [1] "synchronous"
    
     $metagenome$query$attributes
     $metagenome$query$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $metagenome$query$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $metagenome$query$attributes$version
     [1] "integer" "version of the object"
    
     $metagenome$query$attributes$data
     $metagenome$query$attributes$data[[1]]
     [1] "list"
    
     $metagenome$query$attributes$data[[2]]
     $metagenome$query$attributes$data[[2]][[1]]
     [1] "object"
    
     $metagenome$query$attributes$data[[2]][[2]]
     $metagenome$query$attributes$data[[2]][[2]][[1]]
     $metagenome$query$attributes$data[[2]][[2]][[1]]$PI_firstname
     [1] "string" "principal investigator's first name"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$status
     $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[1]]
     [1] "cv"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]]
     $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]][[1]]
     [1] "public" "metagenome is public"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$status[[2]][[2]]
     [1] "private" "metagenome is private"
    
    
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$sequence_type
     [1] "string" "sequencing type"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$collection_date
     [1] "string" "date sample collected"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$feature
     [1] "string" "environmental feature, EnvO term"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$PI_lastname
     [1] "string" "principal investigator's last name"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$latitude
     [1] "string" "latitude where sample taken"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$biome
     [1] "string" "environmental biome, EnvO term"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$id
     [1] "string" "unique metagenome identifier"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$project_name
     [1] "string"
     [2] "name of project containing metagenome"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$project_id
     [1] "string" "id of project containing metagenome"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$country
     [1] "string" "country where sample taken"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$env_package_type
     [1] "string"
     [2] "enviromental package of sample, GSC term"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$longitude
     [1] "string" "longitude where sample taken"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$location
     [1] "string" "location where sample taken"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$name
     [1] "string" "name of metagenome"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$seq_method
     [1] "string" "sequencing method"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$created
     [1] "date"
     [2] "time the metagenome was first created"
    
     $metagenome$query$attributes$data[[2]][[2]][[1]]$material
     [1] "string" "environmental material, EnvO term"
    
    
     $metagenome$query$attributes$data[[2]][[2]][[2]]
     [1] "metagenome object"
    
    
    
    
     $metagenome$query$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
     $metagenome$query$attributes$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $metagenome$query$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $metagenome$query$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $metagenome$query$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
    
    
     $metagenome$instance
     $metagenome$instance$request
     [1] "http://api.metagenomics.anl.gov/metagenome/{ID}"
    
     $metagenome$instance$example
     [1] "http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata"
     [2] "retrieve all metadata for metagenome mgm4447943.3"
    
     $metagenome$instance$name
     [1] "instance"
    
     $metagenome$instance$description
     [1] "Returns a single data object."
    
     $metagenome$instance$parameters
     $metagenome$instance$parameters$body
     named list()
    
     $metagenome$instance$parameters$required
     $metagenome$instance$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $metagenome$instance$parameters$options
     $metagenome$instance$parameters$options$verbosity
     $metagenome$instance$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $metagenome$instance$parameters$options$verbosity[[2]]
     $metagenome$instance$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $metagenome$instance$parameters$options$verbosity[[2]][[2]]
     [1] "metadata" "returns minimal with metadata"
    
     $metagenome$instance$parameters$options$verbosity[[2]][[3]]
     [1] "stats" "returns minimal with statistics"
    
     $metagenome$instance$parameters$options$verbosity[[2]][[4]]
     [1] "full" "returns all metadata and statistics"
    
    
    
    
    
     $metagenome$instance$method
     [1] "GET"
    
     $metagenome$instance$type
     [1] "synchronous"
    
     $metagenome$instance$attributes
     $metagenome$instance$attributes$statistics
     [1] "hash"
     [2] "key value pairs describing statistics"
    
     $metagenome$instance$attributes$status
     $metagenome$instance$attributes$status[[1]]
     [1] "cv"
    
     $metagenome$instance$attributes$status[[2]]
     $metagenome$instance$attributes$status[[2]][[1]]
     [1] "public" "metagenome is public"
    
     $metagenome$instance$attributes$status[[2]][[2]]
     [1] "private" "metagenome is private"
    
    
    
     $metagenome$instance$attributes$version
     [1] "integer" "version of the metagenome"
    
     $metagenome$instance$attributes$project
     [1] "reference project" "reference to the project object"
    
     $metagenome$instance$attributes$name
     [1] "string" "name of metagenome"
    
     $metagenome$instance$attributes$sequence_type
     [1] "string" "sequencing type"
    
     $metagenome$instance$attributes$library
     [1] "reference library"
     [2] "reference to the related library object"
    
     $metagenome$instance$attributes$created
     [1] "date"
     [2] "time the metagenome was first created"
    
     $metagenome$instance$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $metagenome$instance$attributes$id
     [1] "string" "unique metagenome identifier"
    
     $metagenome$instance$attributes$sample
     [1] "reference sample"
     [2] "reference to the related sample object"
    
     $metagenome$instance$attributes$metadata
     [1] "hash"
     [2] "key value pairs describing all metadata"
    
     $metagenome$instance$attributes$mixs
     [1] "hash"
     [2] "key value pairs describing MIxS metadata"
    
    
    
    
     $profile
     $profile$info
     $profile$info$parameters
     $profile$info$parameters$body
     named list()
    
     $profile$info$parameters$required
     named list()
    
     $profile$info$parameters$options
     named list()
    
    
     $profile$info$request
     [1] "http://api.metagenomics.anl.gov/profile"
    
     $profile$info$name
     [1] "info"
    
     $profile$info$type
     [1] "synchronous"
    
     $profile$info$method
     [1] "GET"
    
     $profile$info$attributes
     [1] "self"
    
     $profile$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $profile$instance
     $profile$instance$parameters
     $profile$instance$parameters$body
     named list()
    
     $profile$instance$parameters$required
     $profile$instance$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $profile$instance$parameters$options
     $profile$instance$parameters$options$source
     $profile$instance$parameters$options$source[[1]]
     [1] "cv"
    
     $profile$instance$parameters$options$source[[2]]
     $profile$instance$parameters$options$source[[2]][[1]]
     [1] "M5NR"
    
     $profile$instance$parameters$options$source[[2]][[2]]
     [1] "RefSeq"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[3]]
     [1] "GenBank"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[4]]
     [1] "IMG"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[5]]
     [1] "SEED"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[6]]
     [1] "TrEMBL"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[7]]
     [1] "SwissProt"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[8]]
     [1] "PATRIC"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[9]]
     [1] "KEGG"
     [2] "protein database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[10]]
     [1] "M5RNA"
    
     $profile$instance$parameters$options$source[[2]][[11]]
     [1] "RDP"
     [2] "RNA database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[12]]
     [1] "Greengenes"
     [2] "RNA database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[13]]
     [1] "LSU"
     [2] "RNA database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[14]]
     [1] "SSU"
     [2] "RNA database, type organism, function, feature"
    
     $profile$instance$parameters$options$source[[2]][[15]]
     [1] "Subsystems"
     [2] "ontology database, type ontology only"
    
     $profile$instance$parameters$options$source[[2]][[16]]
     [1] "NOG"
     [2] "ontology database, type ontology only"
    
     $profile$instance$parameters$options$source[[2]][[17]]
     [1] "COG"
     [2] "ontology database, type ontology only"
    
     $profile$instance$parameters$options$source[[2]][[18]]
     [1] "KO"
     [2] "ontology database, type ontology only"
    
    
    
     $profile$instance$parameters$options$length
     [1] "int"
     [2] "value for minimum alignment length cutoff: default is 15"
    
     $profile$instance$parameters$options$identity
     [1] "int"
     [2] "percent value for minimum % identity cutoff: default is 60"
    
     $profile$instance$parameters$options$evalue
     [1] "int"
     [2] "negative exponent value for maximum e-value cutoff: default is 5"
    
     $profile$instance$parameters$options$type
     $profile$instance$parameters$options$type[[1]]
     [1] "cv"
    
     $profile$instance$parameters$options$type[[2]]
     $profile$instance$parameters$options$type[[2]][[1]]
     [1] "organism" "return organism data"
    
     $profile$instance$parameters$options$type[[2]][[2]]
     [1] "function" "return functional data"
    
     $profile$instance$parameters$options$type[[2]][[3]]
     [1] "feature" "return feature data"
    
    
    
     $profile$instance$parameters$options$hit_type
     $profile$instance$parameters$options$hit_type[[1]]
     [1] "cv"
    
     $profile$instance$parameters$options$hit_type[[2]]
     $profile$instance$parameters$options$hit_type[[2]][[1]]
     [1] "all"
     [2] "returns results based on all organisms that map to top hit per read-feature"
    
     $profile$instance$parameters$options$hit_type[[2]][[2]]
     [1] "single"
     [2] "returns results based on a single organism for top hit per read-feature"
    
     $profile$instance$parameters$options$hit_type[[2]][[3]]
     [1] "lca"
     [2] "returns results based on the Least Common Ancestor for all organisms (M5NR+M5RNA only) that map to hits from a read-feature"
    
    
    
    
    
     $profile$instance$name
     [1] "instance"
    
     $profile$instance$type
     [1] "synchronous"
    
     $profile$instance$method
     [1] "GET"
    
     $profile$instance$attributes
     $profile$instance$attributes$generated_by
     [1] "string" "identifier of the data generator"
    
     $profile$instance$attributes$matrix_type
     [1] "string"
     [2] "type of the data encoding matrix (dense or sparse)"
    
     $profile$instance$attributes$date
     [1] "date" "time the output data was generated"
    
     $profile$instance$attributes$data
     $profile$instance$attributes$data[[1]]
     [1] "list"
    
     $profile$instance$attributes$data[[2]]
     $profile$instance$attributes$data[[2]][[1]]
     [1] "list"
    
     $profile$instance$attributes$data[[2]][[2]]
     [1] "float" "the matrix values"
    
    
    
     $profile$instance$attributes$rows
     $profile$instance$attributes$rows[[1]]
     [1] "list"
    
     $profile$instance$attributes$rows[[2]]
     $profile$instance$attributes$rows[[2]][[1]]
     [1] "object"
    
     $profile$instance$attributes$rows[[2]][[2]]
     $profile$instance$attributes$rows[[2]][[2]][[1]]
     $profile$instance$attributes$rows[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $profile$instance$attributes$rows[[2]][[2]][[1]]$id
     [1] "string" "unique identifier"
    
    
     $profile$instance$attributes$rows[[2]][[2]][[2]]
     [1] "rows object"
    
    
    
    
     $profile$instance$attributes$matrix_element_type
     [1] "string"
     [2] "data type of the elements in the return matrix"
    
     $profile$instance$attributes$format_url
     [1] "string" "url to the format specification"
    
     $profile$instance$attributes$format
     [1] "string" "format specification name"
    
     $profile$instance$attributes$columns
     $profile$instance$attributes$columns[[1]]
     [1] "list"
    
     $profile$instance$attributes$columns[[2]]
     $profile$instance$attributes$columns[[2]][[1]]
     [1] "object"
    
     $profile$instance$attributes$columns[[2]][[2]]
     $profile$instance$attributes$columns[[2]][[2]][[1]]
     $profile$instance$attributes$columns[[2]][[2]][[1]]$metadata
     [1] "hash"
     [2] "list of metadata, contains the metagenome"
    
     $profile$instance$attributes$columns[[2]][[2]][[1]]$id
     [1] "string" "unique identifier"
    
    
     $profile$instance$attributes$columns[[2]][[2]][[2]]
     [1] "columns object"
    
    
    
    
     $profile$instance$attributes$id
     [1] "string" "unique object identifier"
    
     $profile$instance$attributes$type
     [1] "string"
     [2] "type of the data in the return table (taxon, function or gene)"
    
     $profile$instance$attributes$shape
     $profile$instance$attributes$shape[[1]]
     [1] "list"
    
     $profile$instance$attributes$shape[[2]]
     [1] "integer"
     [2] "list of the dimension sizes of the return matrix"
    
    
    
     $profile$instance$description
     [1] "Returns a single data object in BIOM format"
    
    
    
     $project
     $project$info
     $project$info$parameters
     $project$info$parameters$body
     named list()
    
     $project$info$parameters$required
     named list()
    
     $project$info$parameters$options
     named list()
    
    
     $project$info$request
     [1] "http://api.metagenomics.anl.gov/project"
    
     $project$info$name
     [1] "info"
    
     $project$info$type
     [1] "synchronous"
    
     $project$info$method
     [1] "GET"
    
     $project$info$attributes
     [1] "self"
    
     $project$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $project$query
     $project$query$request
     [1] "http://api.metagenomics.anl.gov/project"
    
     $project$query$example
     [1] "http://api.metagenomics.anl.gov/project?limit=20&order=name"
     [2] "retrieve the first 20 projects ordered by name"
    
     $project$query$name
     [1] "query"
    
     $project$query$description
     [1] "Returns a set of data matching the query criteria."
    
     $project$query$parameters
     $project$query$parameters$body
     named list()
    
     $project$query$parameters$required
     named list()
    
     $project$query$parameters$options
     $project$query$parameters$options$verbosity
     $project$query$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $project$query$parameters$options$verbosity[[2]]
     $project$query$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $project$query$parameters$options$verbosity[[2]][[2]]
     [1] "verbose" "returns all metadata"
    
     $project$query$parameters$options$verbosity[[2]][[3]]
     [1] "full" "returns all metadata and references"
    
    
    
     $project$query$parameters$options$order
     $project$query$parameters$options$order[[1]]
     [1] "cv"
    
     $project$query$parameters$options$order[[2]]
     $project$query$parameters$options$order[[2]][[1]]
     [1] "id" "return data objects ordered by id"
    
     $project$query$parameters$options$order[[2]][[2]]
     [1] "name" "return data objects ordered by name"
    
    
    
     $project$query$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $project$query$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $project$query$method
     [1] "GET"
    
     $project$query$type
     [1] "synchronous"
    
     $project$query$attributes
     $project$query$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $project$query$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $project$query$attributes$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $project$query$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $project$query$attributes$data
     $project$query$attributes$data[[1]]
     [1] "list"
    
     $project$query$attributes$data[[2]]
     $project$query$attributes$data[[2]][[1]]
     [1] "object"
    
     $project$query$attributes$data[[2]][[2]]
     $project$query$attributes$data[[2]][[2]][[1]]
     $project$query$attributes$data[[2]][[2]][[1]]$status
     $project$query$attributes$data[[2]][[2]][[1]]$status[[1]]
     [1] "cv"
    
     $project$query$attributes$data[[2]][[2]][[1]]$status[[2]]
     $project$query$attributes$data[[2]][[2]][[1]]$status[[2]][[1]]
     [1] "public" "object is public"
    
     $project$query$attributes$data[[2]][[2]][[1]]$status[[2]][[2]]
     [1] "private" "object is private"
    
    
    
     $project$query$attributes$data[[2]][[2]][[1]]$version
     [1] "integer" "version of the object"
    
     $project$query$attributes$data[[2]][[2]][[1]]$name
     [1] "string" "human readable identifier"
    
     $project$query$attributes$data[[2]][[2]][[1]]$description
     [1] "string"
     [2] "a short, comprehensive description of the project"
    
     $project$query$attributes$data[[2]][[2]][[1]]$metagenomes
     $project$query$attributes$data[[2]][[2]][[1]]$metagenomes[[1]]
     [1] "list"
    
     $project$query$attributes$data[[2]][[2]][[1]]$metagenomes[[2]]
     [1] "reference metagenome"
     [2] "a list of references to the related metagenome objects"
    
    
     $project$query$attributes$data[[2]][[2]][[1]]$libraries
     $project$query$attributes$data[[2]][[2]][[1]]$libraries[[1]]
     [1] "list"
    
     $project$query$attributes$data[[2]][[2]][[1]]$libraries[[2]]
     [1] "reference library"
     [2] "a list of references to the related library objects"
    
    
     $project$query$attributes$data[[2]][[2]][[1]]$created
     [1] "date" "time the object was first created"
    
     $project$query$attributes$data[[2]][[2]][[1]]$samples
     $project$query$attributes$data[[2]][[2]][[1]]$samples[[1]]
     [1] "list"
    
     $project$query$attributes$data[[2]][[2]][[1]]$samples[[2]]
     [1] "reference sample"
     [2] "a list of references to the related sample objects"
    
    
     $project$query$attributes$data[[2]][[2]][[1]]$funding_source
     [1] "string"
     [2] "the official name of the source of funding of this project"
    
     $project$query$attributes$data[[2]][[2]][[1]]$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $project$query$attributes$data[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $project$query$attributes$data[[2]][[2]][[1]]$id
     [1] "string" "unique object identifier"
    
     $project$query$attributes$data[[2]][[2]][[1]]$pi
     [1] "string"
     [2] "the first and last name of the principal investigator of the project"
    
    
     $project$query$attributes$data[[2]][[2]][[2]]
     [1] "list of the project objects"
    
    
    
    
     $project$query$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
     $project$query$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
    
    
     $project$instance
     $project$instance$request
     [1] "http://api.metagenomics.anl.gov/project/{ID}"
    
     $project$instance$example
     [1] "http://api.metagenomics.anl.gov/project/mgp128?verbosity=full"
     [2] "retrieve all data for project mgp128"
    
     $project$instance$name
     [1] "instance"
    
     $project$instance$description
     [1] "Returns a single data object."
    
     $project$instance$parameters
     $project$instance$parameters$body
     named list()
    
     $project$instance$parameters$required
     $project$instance$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $project$instance$parameters$options
     $project$instance$parameters$options$verbosity
     $project$instance$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $project$instance$parameters$options$verbosity[[2]]
     $project$instance$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $project$instance$parameters$options$verbosity[[2]][[2]]
     [1] "verbose" "returns all metadata"
    
     $project$instance$parameters$options$verbosity[[2]][[3]]
     [1] "full" "returns all metadata and references"
    
    
    
    
    
     $project$instance$method
     [1] "GET"
    
     $project$instance$type
     [1] "synchronous"
    
     $project$instance$attributes
     $project$instance$attributes$status
     $project$instance$attributes$status[[1]]
     [1] "cv"
    
     $project$instance$attributes$status[[2]]
     $project$instance$attributes$status[[2]][[1]]
     [1] "public" "object is public"
    
     $project$instance$attributes$status[[2]][[2]]
     [1] "private" "object is private"
    
    
    
     $project$instance$attributes$version
     [1] "integer" "version of the object"
    
     $project$instance$attributes$name
     [1] "string" "human readable identifier"
    
     $project$instance$attributes$description
     [1] "string"
     [2] "a short, comprehensive description of the project"
    
     $project$instance$attributes$metagenomes
     $project$instance$attributes$metagenomes[[1]]
     [1] "list"
    
     $project$instance$attributes$metagenomes[[2]]
     [1] "reference metagenome"
     [2] "a list of references to the related metagenome objects"
    
    
     $project$instance$attributes$libraries
     $project$instance$attributes$libraries[[1]]
     [1] "list"
    
     $project$instance$attributes$libraries[[2]]
     [1] "reference library"
     [2] "a list of references to the related library objects"
    
    
     $project$instance$attributes$created
     [1] "date" "time the object was first created"
    
     $project$instance$attributes$samples
     $project$instance$attributes$samples[[1]]
     [1] "list"
    
     $project$instance$attributes$samples[[2]]
     [1] "reference sample"
     [2] "a list of references to the related sample objects"
    
    
     $project$instance$attributes$funding_source
     [1] "string"
     [2] "the official name of the source of funding of this project"
    
     $project$instance$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $project$instance$attributes$metadata
     [1] "hash" "key value pairs describing metadata"
    
     $project$instance$attributes$id
     [1] "string" "unique object identifier"
    
     $project$instance$attributes$pi
     [1] "string"
     [2] "the first and last name of the principal investigator of the project"
    
    
    
    
     $sample
     $sample$info
     $sample$info$parameters
     $sample$info$parameters$body
     named list()
    
     $sample$info$parameters$required
     named list()
    
     $sample$info$parameters$options
     named list()
    
    
     $sample$info$request
     [1] "http://api.metagenomics.anl.gov/sample"
    
     $sample$info$name
     [1] "info"
    
     $sample$info$type
     [1] "synchronous"
    
     $sample$info$method
     [1] "GET"
    
     $sample$info$attributes
     [1] "self"
    
     $sample$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $sample$query
     $sample$query$request
     [1] "http://api.metagenomics.anl.gov/sample"
    
     $sample$query$example
     [1] "http://api.metagenomics.anl.gov/sample?limit=20&order=name"
     [2] "retrieve the first 20 samples ordered by name"
    
     $sample$query$name
     [1] "query"
    
     $sample$query$description
     [1] "Returns a set of data matching the query criteria."
    
     $sample$query$parameters
     $sample$query$parameters$body
     named list()
    
     $sample$query$parameters$required
     named list()
    
     $sample$query$parameters$options
     $sample$query$parameters$options$order
     $sample$query$parameters$options$order[[1]]
     [1] "cv"
    
     $sample$query$parameters$options$order[[2]]
     $sample$query$parameters$options$order[[2]][[1]]
     [1] "id" "return data objects ordered by id"
    
     $sample$query$parameters$options$order[[2]][[2]]
     [1] "name" "return data objects ordered by name"
    
    
    
     $sample$query$parameters$options$limit
     [1] "integer" "maximum number of items requested"
    
     $sample$query$parameters$options$offset
     [1] "integer"
     [2] "zero based index of the first data object to be returned"
    
    
    
     $sample$query$method
     [1] "GET"
    
     $sample$query$type
     [1] "synchronous"
    
     $sample$query$attributes
     $sample$query$attributes$`next`
     [1] "uri"
     [2] "link to the previous set or null if this is the first set"
    
     $sample$query$attributes$prev
     [1] "uri"
     [2] "link to the next set or null if this is the last set"
    
     $sample$query$attributes$order
     [1] "string"
     [2] "name of the attribute the returned data is ordered by"
    
     $sample$query$attributes$limit
     [1] "integer"
     [2] "maximum number of data items returned, default is 10"
    
     $sample$query$attributes$data
     $sample$query$attributes$data[[1]]
     [1] "list"
    
     $sample$query$attributes$data[[2]]
     $sample$query$attributes$data[[2]][[1]]
     [1] "object"
    
     $sample$query$attributes$data[[2]][[2]]
     $sample$query$attributes$data[[2]][[2]][[1]]
     $sample$query$attributes$data[[2]][[2]][[1]]$version
     [1] "integer" "version of the object"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$project
     [1] "reference project"
     [2] "reference to the project of this sample"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$name
     [1] "string" "human readable identifier"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes
     $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes[[1]]
     [1] "list"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$metagenomes[[2]]
     [1] "reference metagenome"
     [2] "a list of references to the related metagenome objects"
    
    
     $sample$query$attributes$data[[2]][[2]][[1]]$libraries
     $sample$query$attributes$data[[2]][[2]][[1]]$libraries[[1]]
     [1] "list"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$libraries[[2]]
     [1] "reference library"
     [2] "a list of references to the related library objects"
    
    
     $sample$query$attributes$data[[2]][[2]][[1]]$created
     [1] "date" "time the object was first created"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[1]]
     [1] "object"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]]
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$created
     [1] "date" "creation date"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$name
     [1] "string" "name of the package"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$id
     [1] "string" "unique package identifier"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$type
     [1] "string" "package type"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
     $sample$query$attributes$data[[2]][[2]][[1]]$env_package[[2]][[2]]
     [1] "environmental package object"
    
    
    
     $sample$query$attributes$data[[2]][[2]][[1]]$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$id
     [1] "string" "unique object identifier"
    
     $sample$query$attributes$data[[2]][[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
     $sample$query$attributes$data[[2]][[2]][[2]]
     [1] "list of sample objects"
    
    
    
    
     $sample$query$attributes$offset
     [1] "integer"
     [2] "zero based index of the first returned data item"
    
     $sample$query$attributes$total_count
     [1] "integer"
     [2] "total number of available data items"
    
    
    
     $sample$instance
     $sample$instance$request
     [1] "http://api.metagenomics.anl.gov/sample/{ID}"
    
     $sample$instance$example
     [1] "http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full"
     [2] "retrieve all data for sample mgs25823"
    
     $sample$instance$name
     [1] "instance"
    
     $sample$instance$description
     [1] "Returns a single data object."
    
     $sample$instance$parameters
     $sample$instance$parameters$body
     named list()
    
     $sample$instance$parameters$required
     $sample$instance$parameters$required$id
     [1] "string" "unique object identifier"
    
    
     $sample$instance$parameters$options
     $sample$instance$parameters$options$verbosity
     $sample$instance$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $sample$instance$parameters$options$verbosity[[2]]
     $sample$instance$parameters$options$verbosity[[2]][[1]]
     [1] "minimal" "returns only minimal information"
    
     $sample$instance$parameters$options$verbosity[[2]][[2]]
     [1] "verbose" "returns all metadata"
    
     $sample$instance$parameters$options$verbosity[[2]][[3]]
     [1] "full" "returns all metadata and references"
    
    
    
    
    
     $sample$instance$method
     [1] "GET"
    
     $sample$instance$type
     [1] "synchronous"
    
     $sample$instance$attributes
     $sample$instance$attributes$version
     [1] "integer" "version of the object"
    
     $sample$instance$attributes$project
     [1] "reference project"
     [2] "reference to the project of this sample"
    
     $sample$instance$attributes$name
     [1] "string" "human readable identifier"
    
     $sample$instance$attributes$metagenomes
     $sample$instance$attributes$metagenomes[[1]]
     [1] "list"
    
     $sample$instance$attributes$metagenomes[[2]]
     [1] "reference metagenome"
     [2] "a list of references to the related metagenome objects"
    
    
     $sample$instance$attributes$libraries
     $sample$instance$attributes$libraries[[1]]
     [1] "list"
    
     $sample$instance$attributes$libraries[[2]]
     [1] "reference library"
     [2] "a list of references to the related library objects"
    
    
     $sample$instance$attributes$created
     [1] "date" "time the object was first created"
    
     $sample$instance$attributes$env_package
     $sample$instance$attributes$env_package[[1]]
     [1] "object"
    
     $sample$instance$attributes$env_package[[2]]
     $sample$instance$attributes$env_package[[2]][[1]]
     $sample$instance$attributes$env_package[[2]][[1]]$created
     [1] "date" "creation date"
    
     $sample$instance$attributes$env_package[[2]][[1]]$name
     [1] "string" "name of the package"
    
     $sample$instance$attributes$env_package[[2]][[1]]$id
     [1] "string" "unique package identifier"
    
     $sample$instance$attributes$env_package[[2]][[1]]$type
     [1] "string" "package type"
    
     $sample$instance$attributes$env_package[[2]][[1]]$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
     $sample$instance$attributes$env_package[[2]][[2]]
     [1] "environmental package object"
    
    
    
     $sample$instance$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $sample$instance$attributes$id
     [1] "string" "unique object identifier"
    
     $sample$instance$attributes$metadata
     [1] "hash" "key value pairs describing metadata"
    
    
    
    
     $server
     $server$info
     $server$info$parameters
     $server$info$parameters$body
     named list()
    
     $server$info$parameters$required
     named list()
    
     $server$info$parameters$options
     named list()
    
    
     $server$info$request
     [1] "http://api.metagenomics.anl.gov/server"
    
     $server$info$name
     [1] "info"
    
     $server$info$type
     [1] "synchronous"
    
     $server$info$method
     [1] "GET"
    
     $server$info$attributes
     [1] "self"
    
     $server$info$description
     [1] "Returns the server information."
    
    
     $server$instance
     $server$instance$request
     [1] "http://api.metagenomics.anl.gov/server/{ID}"
    
     $server$instance$example
     [1] "curl -X GET \"http://api.metagenomics.anl.gov/server/MG-RAST\""
     [2] "info for the MG-RAST server"
    
     $server$instance$name
     [1] "instance"
    
     $server$instance$description
     [1] "Returns a single user object."
    
     $server$instance$parameters
     $server$instance$parameters$body
     named list()
    
     $server$instance$parameters$required
     $server$instance$parameters$required$id
     [1] "string" "unique server ID"
    
    
     $server$instance$parameters$options
     named list()
    
    
     $server$instance$method
     [1] "GET"
    
     $server$instance$type
     [1] "synchronous"
    
     $server$instance$attributes
     $server$instance$attributes$info
     [1] "string"
     [2] "informational text, i.e. downtime warnings"
    
     $server$instance$attributes$basepairs
     [1] "integer" "total number of basepairs"
    
     $server$instance$attributes$status
     [1] "string" "status of the server"
    
     $server$instance$attributes$version
     [1] "string" "version number of the server"
    
     $server$instance$attributes$url
     [1] "uri"
     [2] "resource location of this object instance"
    
     $server$instance$attributes$id
     [1] "string" "unique identifier of this server"
    
     $server$instance$attributes$public_metagenomes
     [1] "integer" "total number of public metagenomes"
    
     $server$instance$attributes$metagenomes
     [1] "integer" "total number of metagenomes"
    
     $server$instance$attributes$sequences
     [1] "integer" "total number of sequences"
    
    
    
    
     $validation
     $validation$info
     $validation$info$parameters
     $validation$info$parameters$body
     named list()
    
     $validation$info$parameters$required
     named list()
    
     $validation$info$parameters$options
     named list()
    
    
     $validation$info$request
     [1] "http://api.metagenomics.anl.gov/validation"
    
     $validation$info$name
     [1] "info"
    
     $validation$info$type
     [1] "synchronous"
    
     $validation$info$method
     [1] "GET"
    
     $validation$info$attributes
     [1] "self"
    
     $validation$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $validation$template
     $validation$template$request
     [1] "http://api.metagenomics.anl.gov/validation/template/{ID}"
    
     $validation$template$example
     [1] "http://api.metagenomics.anl.gov/validation/template/"
     [2] "validate the communities metagenomics template"
    
     $validation$template$name
     [1] "template"
    
     $validation$template$description
     [1] "Checks if the referenced JSON structure is a valid template"
    
     $validation$template$parameters
     $validation$template$parameters$body
     named list()
    
     $validation$template$parameters$required
     $validation$template$parameters$required$id
     [1] "string" "SHOCK template id"
    
    
     $validation$template$parameters$options
     named list()
    
    
     $validation$template$method
     [1] "GET"
    
     $validation$template$type
     [1] "synchronous"
    
     $validation$template$attributes
     $validation$template$attributes$error
     $validation$template$attributes$error[[1]]
     [1] "array"
    
     $validation$template$attributes$error[[2]]
     [1] "string" "array of invalid entries"
    
    
     $validation$template$attributes$valid
     [1] "boolean"
     [2] "boolean indicating whether the examined template is valid or not"
    
    
    
     $validation$data
     $validation$data$request
     [1] "http://api.metagenomics.anl.gov/validation/data/{ID}"
    
     $validation$data$example
     [1] "http://api.metagenomics.anl.gov/validation/data/?template="
     [2] "validate a JSON data structure against the MG-RAST metagenome metadata template"
    
     $validation$data$name
     [1] "data"
    
     $validation$data$description
     [1] "Returns a single data object."
    
     $validation$data$parameters
     $validation$data$parameters$body
     named list()
    
     $validation$data$parameters$required
     $validation$data$parameters$required$id
     [1] "string" "SHOCK data id"
    
    
     $validation$data$parameters$options
     $validation$data$parameters$options$template
     [1] "string"
     [2] "SHOCK template id, default is MG-RAST metagenome metadata template"
    
    
    
     $validation$data$method
     [1] "GET"
    
     $validation$data$type
     [1] "synchronous"
    
     $validation$data$attributes
     $validation$data$attributes$error
     $validation$data$attributes$error[[1]]
     [1] "array"
    
     $validation$data$attributes$error[[2]]
     [1] "string" "array of invalid entries"
    
    
     $validation$data$attributes$valid
     [1] "boolean"
     [2] "boolean indicating whether the examined template is valid or not"
    
    
    
    
     $status
     $status$info
     $status$info$parameters
     $status$info$parameters$body
     named list()
    
     $status$info$parameters$required
     named list()
    
     $status$info$parameters$options
     named list()
    
    
     $status$info$request
     [1] "http://api.metagenomics.anl.gov/status"
    
     $status$info$name
     [1] "info"
    
     $status$info$type
     [1] "synchronous"
    
     $status$info$method
     [1] "GET"
    
     $status$info$attributes
     [1] "self"
    
     $status$info$description
     [1] "Returns description of parameters and attributes."
    
    
     $status$instance
     $status$instance$request
     [1] "http://api.metagenomics.anl.gov/status/{TOKEN}"
    
     $status$instance$example
     [1] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/status/12345\""
     [2] "data for asynchronous call with ID 12345"
    
     $status$instance$name
     [1] "instance"
    
     $status$instance$description
     [1] "Returns a single data object."
    
     $status$instance$parameters
     $status$instance$parameters$body
     named list()
    
     $status$instance$parameters$required
     $status$instance$parameters$required$id
     [1] "string" "unique process id"
    
    
     $status$instance$parameters$options
     $status$instance$parameters$options$verbosity
     $status$instance$parameters$options$verbosity[[1]]
     [1] "cv"
    
     $status$instance$parameters$options$verbosity[[2]]
     $status$instance$parameters$options$verbosity[[2]][[1]]
     [1] "full" "returns all connected metadata"
    
     $status$instance$parameters$options$verbosity[[2]][[2]]
     [1] "minimal" "returns only minimal information"
    
    
    
    
    
     $status$instance$method
     [1] "GET"
    
     $status$instance$type
     [1] "synchronous"
    
     $status$instance$attributes
     $status$instance$attributes$status
     $status$instance$attributes$status[[1]]
     [1] "string"
    
     $status$instance$attributes$status[[2]]
     [1] "cv"
    
     $status$instance$attributes$status[[3]]
     $status$instance$attributes$status[[3]][[1]]
     [1] "processing" "process is still computing"
    
     $status$instance$attributes$status[[3]][[2]]
     [1] "done" "process is done computing"
    
    
    
     $status$instance$attributes$url
     [1] "url"
     [2] "resource location of this object instance"
    
     $status$instance$attributes$data
     [1] "hash"
     [2] "if status is done, data holds the result, otherwise data is not present"
    
     $status$instance$attributes$id
     [1] "integer" "process id"
    
    
    
    
     > API <- get ("API", envir=.MGRAST)
     >
     > #-----------------------------------------------------------------------------
     > # test docs
     > #-----------------------------------------------------------------------------
     >
     > doc.MGRAST()
     List of 15
     $ annotation:List of 3
     $ compute :List of 2
     $ download :List of 3
     $ inbox :List of 2
     $ library :List of 3
     $ m5nr :List of 10
     $ matrix :List of 4
     $ metadata :List of 6
     $ metagenome:List of 3
     $ profile :List of 2
     $ project :List of 3
     $ sample :List of 3
     $ server :List of 2
     $ validation:List of 3
     $ status :List of 2
     > doc.MGRAST(2)
     List of 15
     $ annotation:List of 3
     ..$ info :List of 7
     ..$ sequence :List of 8
     ..$ similarity:List of 8
     $ compute :List of 2
     ..$ info :List of 7
     ..$ alphadiversity:List of 8
     $ download :List of 3
     ..$ info :List of 7
     ..$ instance:List of 8
     ..$ setlist :List of 8
     $ inbox :List of 2
     ..$ info:List of 7
     ..$ view:List of 8
     $ library :List of 3
     ..$ info :List of 7
     ..$ query :List of 8
     ..$ instance:List of 8
     $ m5nr :List of 10
     ..$ info :List of 7
     ..$ ontology :List of 8
     ..$ taxonomy :List of 8
     ..$ sources :List of 8
     ..$ accession:List of 8
     ..$ alias :List of 8
     ..$ md5 :List of 8
     ..$ function :List of 8
     ..$ organism :List of 8
     ..$ sequence :List of 8
     $ matrix :List of 4
     ..$ info :List of 7
     ..$ organism:List of 8
     ..$ function:List of 8
     ..$ feature :List of 8
     $ metadata :List of 6
     ..$ info :List of 7
     ..$ template:List of 8
     ..$ cv :List of 8
     ..$ ontology:List of 8
     ..$ export :List of 8
     ..$ validate:List of 8
     $ metagenome:List of 3
     ..$ info :List of 7
     ..$ query :List of 8
     ..$ instance:List of 8
     $ profile :List of 2
     ..$ info :List of 7
     ..$ instance:List of 6
     $ project :List of 3
     ..$ info :List of 7
     ..$ query :List of 8
     ..$ instance:List of 8
     $ sample :List of 3
     ..$ info :List of 7
     ..$ query :List of 8
     ..$ instance:List of 8
     $ server :List of 2
     ..$ info :List of 7
     ..$ instance:List of 8
     $ validation:List of 3
     ..$ info :List of 7
     ..$ template:List of 8
     ..$ data :List of 8
     $ status :List of 2
     ..$ info :List of 7
     ..$ instance:List of 8
     > doc.MGRAST(3)
     List of 15
     $ annotation:List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/annotation"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ sequence :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/annotation/sequence/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt" "all annotated read sequences from mgm4447943.3 with hits in SwissProt organisms at evaule < e-10"
     .. ..$ name : chr "sequence"
     .. ..$ description: chr "tab deliminted annotated sequence stream"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "stream"
     .. ..$ attributes :List of 1
     ..$ similarity:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/annotation/similarity/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO" "all annotated read blat stats from mgm4447943.3 with hits in KO functions at % identity > 80"
     .. ..$ name : chr "similarity"
     .. ..$ description: chr "tab deliminted blast m8 with annotation"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "stream"
     .. ..$ attributes :List of 1
     $ compute :List of 2
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/compute"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ alphadiversity:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/compute/alphadiversity/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/compute/alphadiversity/mgm4447943.3?level=order" "retrieve alpha diversity for order taxon"
     .. ..$ name : chr "alphadiversity"
     .. ..$ description: chr "Calculate alpha diversity value for given ID and taxon level."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 3
     $ download :List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/download"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/download/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/download/mgm4447943.3?file=350.1" "download fasta file of genecalled protein sequences (from stage 350)"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single sequence file."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 1
     ..$ setlist :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/download/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/download/mgm4447943.3?stage=650" "view all available files from stage 650"
     .. ..$ name : chr "setlist"
     .. ..$ description: chr "Returns a list of sets of sequence files for the given id."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 7
     $ inbox :List of 2
     ..$ info:List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/inbox"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ view:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/inbox"
     .. ..$ example : chr [1:2] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/inbox\"" "lists the contents of the user inbox, auth is required"
     .. ..$ name : chr "view"
     .. ..$ description: chr "lists the contents of the user inbox"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 4
     $ library :List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/library"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ query :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/library"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/library?limit=20&order=name" "retrieve the first 20 libraries ordered by name"
     .. ..$ name : chr "query"
     .. ..$ description: chr "Returns a set of data matching the query criteria."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 7
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/library/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/library/mgl52924?verbosity=full" "retrieve all data for library mgl52924"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 10
     $ m5nr :List of 10
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ ontology :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/ontology"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/ontology?source=Subsystems&min_level=level3" "retrieve subsystems hierarchy for the top 3 levels"
     .. ..$ name : chr "ontology"
     .. ..$ description: chr "Return functional hierarchy"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 3
     ..$ taxonomy :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/taxonomy"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus" "retrieve all class level taxa that belong to Bacteroidetes"
     .. ..$ name : chr "taxonomy"
     .. ..$ description: chr "Return organism hierarchy"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 3
     ..$ sources :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/sources"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/sources" "retrieve all data sources for M5NR"
     .. ..$ name : chr "sources"
     .. ..$ description: chr "Return all sources in M5NR"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 3
     ..$ accession:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/accession/{id}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/accession/YP_003268079.1" "retrieve M5NR data for accession ID 'YP_003268079.1'"
     .. ..$ name : chr "accession"
     .. ..$ description: chr "Return annotation of given source protein ID"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     ..$ alias :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/alias/{text}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/alias/IPR001478" "retrieve M5NR data for db_xref ID 'IPR001478'"
     .. ..$ name : chr "alias"
     .. ..$ description: chr "Return annotations for alias IDs containing the given text"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     ..$ md5 :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/md5/{id}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro" "retrieve InterPro M5NR data for md5sum '000821a2e2f63df1a3873e4b280002a8'"
     .. ..$ name : chr "md5"
     .. ..$ description: chr "Return annotation(s) or sequence of given md5sum (M5NR ID)"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     ..$ function :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/function/{text}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/function/sulfatase?source=GenBank" "retrieve GenBank M5NR data for function names containing string 'sulfatase'"
     .. ..$ name : chr "function"
     .. ..$ description: chr "Return annotations for function names containing the given text"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     ..$ organism :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/organism/{text}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/organism/akkermansia?source=KEGG" "retrieve KEGG M5NR data for organism names containing string 'akkermansia'"
     .. ..$ name : chr "organism"
     .. ..$ description: chr "Return annotations for organism names containing the given text"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     ..$ sequence :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/m5nr/sequence/{text}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL" "retrieve TrEMBL M5NR data for md5sum of sequence 'MAGENHQWQGSIL'"
     .. ..$ name : chr "sequence"
     .. ..$ description: chr "Return annotation(s) for md5sum (M5NR ID) of given sequence"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 8
     $ matrix :List of 4
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/matrix"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ organism:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/matrix/organism"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
     .. ..$ name : chr "organism"
     .. ..$ description: chr "Returns a BIOM object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous or asynchronous"
     .. ..$ attributes :List of 14
     ..$ function:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/matrix/function"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
     .. ..$ name : chr "function"
     .. ..$ description: chr "Returns a BIOM object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous or asynchronous"
     .. ..$ attributes :List of 14
     ..$ feature :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/matrix/feature"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
     .. ..$ name : chr "feature"
     .. ..$ description: chr "Returns a BIOM object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous or asynchronous"
     .. ..$ attributes :List of 14
     $ metadata :List of 6
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ template:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata/template"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metadata/template" "metadata template"
     .. ..$ name : chr "template"
     .. ..$ description: chr "Returns static template for metadata object relationships and types"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 4
     ..$ cv :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata/cv"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metadata/cv?label=country" "metadata controlled vocabularies"
     .. ..$ name : chr "cv"
     .. ..$ description: chr "Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label"| __truncated__
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 3
     ..$ ontology:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata/ontology"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metadata/ontology?name=biome&version=2013-04-27" "metadata ontology lookup"
     .. ..$ name : chr "ontology"
     .. ..$ description: chr "Returns static ontology used in metadata for the given name and version."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 6
     ..$ export :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata/export/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metadata/export/mgp128" "all metadata for project mgp128"
     .. ..$ name : chr "export"
     .. ..$ description: chr "Returns full nested metadata for a project in same format as template, or metadata for a single metagenome."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 5
     ..$ validate:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metadata/validate"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metadata/validate?category=sample&label=material&value=soil" "check if 'soil' is a vaild term for sample material"
     .. ..$ name : chr "validate"
     .. ..$ description: chr "Validate given metadata value"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 2
     $ metagenome:List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metagenome"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ query :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metagenome"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metagenome?limit=20&order=name" "retrieve the first 20 metagenomes ordered by name"
     .. ..$ name : chr "query"
     .. ..$ description: chr "Returns a set of data matching the query criteria."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 9
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/metagenome/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/metagenome/mgm4447943.3?verbosity=metadata" "retrieve all metadata for metagenome mgm4447943.3"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 13
     $ profile :List of 2
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/profile"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ instance:List of 6
     .. ..$ parameters :List of 3
     .. ..$ name : chr "instance"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes :List of 12
     .. ..$ description: chr "Returns a single data object in BIOM format"
     $ project :List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/project"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ query :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/project"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/project?limit=20&order=name" "retrieve the first 20 projects ordered by name"
     .. ..$ name : chr "query"
     .. ..$ description: chr "Returns a set of data matching the query criteria."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 7
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/project/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/project/mgp128?verbosity=full" "retrieve all data for project mgp128"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 13
     $ sample :List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/sample"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ query :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/sample"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/sample?limit=20&order=name" "retrieve the first 20 samples ordered by name"
     .. ..$ name : chr "query"
     .. ..$ description: chr "Returns a set of data matching the query criteria."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 7
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/sample/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/sample/mgs25823?verbosity=full" "retrieve all data for sample mgs25823"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 10
     $ server :List of 2
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/server"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns the server information."
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/server/{ID}"
     .. ..$ example : chr [1:2] "curl -X GET \"http://api.metagenomics.anl.gov/server/MG-RAST\"" "info for the MG-RAST server"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single user object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 9
     $ validation:List of 3
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/validation"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ template:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/validation/template/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/validation/template/" "validate the communities metagenomics template"
     .. ..$ name : chr "template"
     .. ..$ description: chr "Checks if the referenced JSON structure is a valid template"
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 2
     ..$ data :List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/validation/data/{ID}"
     .. ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/validation/data/?template=" "validate a JSON data structure against the MG-RAST metagenome metadata template"
     .. ..$ name : chr "data"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 2
     $ status :List of 2
     ..$ info :List of 7
     .. ..$ parameters :List of 3
     .. ..$ request : chr "http://api.metagenomics.anl.gov/status"
     .. ..$ name : chr "info"
     .. ..$ type : chr "synchronous"
     .. ..$ method : chr "GET"
     .. ..$ attributes : chr "self"
     .. ..$ description: chr "Returns description of parameters and attributes."
     ..$ instance:List of 8
     .. ..$ request : chr "http://api.metagenomics.anl.gov/status/{TOKEN}"
     .. ..$ example : chr [1:2] "curl -X GET -H \"auth: auth_key\" \"http://api.metagenomics.anl.gov/status/12345\"" "data for asynchronous call with ID 12345"
     .. ..$ name : chr "instance"
     .. ..$ description: chr "Returns a single data object."
     .. ..$ parameters :List of 3
     .. ..$ method : chr "GET"
     .. ..$ type : chr "synchronous"
     .. ..$ attributes :List of 4
     >
     > doc.MGRAST (head="matrix")
     List of 4
     $ info :List of 7
     $ organism:List of 8
     $ function:List of 8
     $ feature :List of 8
     > doc.MGRAST (2, head="matrix")
     List of 4
     $ info :List of 7
     ..$ parameters :List of 3
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix"
     ..$ name : chr "info"
     ..$ type : chr "synchronous"
     ..$ method : chr "GET"
     ..$ attributes : chr "self"
     ..$ description: chr "Returns description of parameters and attributes."
     $ organism:List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/organism"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
     ..$ name : chr "organism"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     $ function:List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/function"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
     ..$ name : chr "function"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     $ feature :List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/feature"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
     ..$ name : chr "feature"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     > doc.MGRAST (3, head="matrix")
     List of 4
     $ info :List of 7
     ..$ parameters :List of 3
     .. ..$ body : Named list()
     .. ..$ required: Named list()
     .. ..$ options : Named list()
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix"
     ..$ name : chr "info"
     ..$ type : chr "synchronous"
     ..$ method : chr "GET"
     ..$ attributes : chr "self"
     ..$ description: chr "Returns description of parameters and attributes."
     $ organism:List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/organism"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of RefSeq organism annotations at family taxa for listed metagenomes at evaule < e-15"
     ..$ name : chr "organism"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     .. ..$ body : Named list()
     .. ..$ required: Named list()
     .. ..$ options :List of 15
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     .. ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     .. ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     .. ..$ date : chr [1:2] "date" "time the output data was generated"
     .. ..$ data :List of 2
     .. ..$ rows :List of 2
     .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     .. ..$ format_url : chr [1:2] "string" "url to the format specification"
     .. ..$ format : chr [1:2] "string" "format specification name"
     .. ..$ columns :List of 2
     .. ..$ url : chr [1:2] "uri" "resource location of this object instance"
     .. ..$ shape :List of 2
     .. ..$ id : chr [1:2] "string" "unique object identifier"
     .. ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ function:List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/function"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3"| __truncated__ "retrieve abundance matrix of Subsystem annotations at level3 for listed metagenomes at % identity > 80, filtere"| __truncated__
     ..$ name : chr "function"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     .. ..$ body : Named list()
     .. ..$ required: Named list()
     .. ..$ options :List of 13
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     .. ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     .. ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     .. ..$ date : chr [1:2] "date" "time the output data was generated"
     .. ..$ data :List of 2
     .. ..$ rows :List of 2
     .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     .. ..$ format_url : chr [1:2] "string" "url to the format specification"
     .. ..$ format : chr [1:2] "string" "format specification name"
     .. ..$ columns :List of 2
     .. ..$ url : chr [1:2] "uri" "resource location of this object instance"
     .. ..$ shape :List of 2
     .. ..$ id : chr [1:2] "string" "unique object identifier"
     .. ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ feature :List of 8
     ..$ request : chr "http://api.metagenomics.anl.gov/matrix/feature"
     ..$ example : chr [1:2] "http://api.metagenomics.anl.gov/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&"| __truncated__ "retrieve e-value matrix of KEGG protein annotations for listed metagenomes at alignment length > 25"
     ..$ name : chr "feature"
     ..$ description: chr "Returns a BIOM object."
     ..$ parameters :List of 3
     .. ..$ body : Named list()
     .. ..$ required: Named list()
     .. ..$ options :List of 11
     ..$ method : chr "GET"
     ..$ type : chr "synchronous or asynchronous"
     ..$ attributes :List of 14
     .. ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     .. ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     .. ..$ date : chr [1:2] "date" "time the output data was generated"
     .. ..$ data :List of 2
     .. ..$ rows :List of 2
     .. ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     .. ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     .. ..$ format_url : chr [1:2] "string" "url to the format specification"
     .. ..$ format : chr [1:2] "string" "format specification name"
     .. ..$ columns :List of 2
     .. ..$ url : chr [1:2] "uri" "resource location of this object instance"
     .. ..$ shape :List of 2
     .. ..$ id : chr [1:2] "string" "unique object identifier"
     .. ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     >
     > doc.MGRAST (stratum="parameters")
     List of 51
     $ annotation.info.parameters :List of 3
     $ annotation.sequence.parameters :List of 3
     $ annotation.similarity.parameters :List of 3
     $ compute.info.parameters :List of 3
     $ compute.alphadiversity.parameters:List of 3
     $ download.info.parameters :List of 3
     $ download.instance.parameters :List of 3
     $ download.setlist.parameters :List of 3
     $ inbox.info.parameters :List of 3
     $ inbox.view.parameters :List of 3
     $ library.info.parameters :List of 3
     $ library.query.parameters :List of 3
     $ library.instance.parameters :List of 3
     $ m5nr.info.parameters :List of 3
     $ m5nr.ontology.parameters :List of 3
     $ m5nr.taxonomy.parameters :List of 3
     $ m5nr.sources.parameters :List of 3
     $ m5nr.accession.parameters :List of 3
     $ m5nr.alias.parameters :List of 3
     $ m5nr.md5.parameters :List of 3
     $ m5nr.function.parameters :List of 3
     $ m5nr.organism.parameters :List of 3
     $ m5nr.sequence.parameters :List of 3
     $ matrix.info.parameters :List of 3
     $ matrix.organism.parameters :List of 3
     $ matrix.function.parameters :List of 3
     $ matrix.feature.parameters :List of 3
     $ metadata.info.parameters :List of 3
     $ metadata.template.parameters :List of 3
     $ metadata.cv.parameters :List of 3
     $ metadata.ontology.parameters :List of 3
     $ metadata.export.parameters :List of 3
     $ metadata.validate.parameters :List of 3
     $ metagenome.info.parameters :List of 3
     $ metagenome.query.parameters :List of 3
     $ metagenome.instance.parameters :List of 3
     $ profile.info.parameters :List of 3
     $ profile.instance.parameters :List of 3
     $ project.info.parameters :List of 3
     $ project.query.parameters :List of 3
     $ project.instance.parameters :List of 3
     $ sample.info.parameters :List of 3
     $ sample.query.parameters :List of 3
     $ sample.instance.parameters :List of 3
     $ server.info.parameters :List of 3
     $ server.instance.parameters :List of 3
     $ validation.info.parameters :List of 3
     $ validation.template.parameters :List of 3
     $ validation.data.parameters :List of 3
     $ status.info.parameters :List of 3
     $ status.instance.parameters :List of 3
     > doc.MGRAST (2, stratum="parameters")
     List of 51
     $ annotation.info.parameters :List of 3
     ..$ body : Named list()
     ..$ options : Named list()
     ..$ required: Named list()
     $ annotation.sequence.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 7
     ..$ required:List of 1
     $ annotation.similarity.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 7
     ..$ required:List of 1
     $ compute.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ compute.alphadiversity.parameters:List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 2
     $ download.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ download.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ download.setlist.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ inbox.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ inbox.view.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options : Named list()
     $ library.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ library.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 4
     $ library.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ m5nr.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ m5nr.ontology.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 6
     $ m5nr.taxonomy.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 5
     $ m5nr.sources.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 1
     $ m5nr.accession.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 4
     $ m5nr.alias.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 6
     $ m5nr.md5.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 7
     $ m5nr.function.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 7
     $ m5nr.organism.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 8
     $ m5nr.sequence.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 5
     $ matrix.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ matrix.organism.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 15
     $ matrix.function.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 13
     $ matrix.feature.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 11
     $ metadata.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metadata.template.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metadata.cv.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 2
     ..$ required: Named list()
     $ metadata.ontology.parameters :List of 3
     ..$ body : Named list()
     ..$ options : Named list()
     ..$ required:List of 2
     $ metadata.export.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options : Named list()
     $ metadata.validate.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 5
     ..$ required: Named list()
     $ metagenome.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metagenome.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 11
     $ metagenome.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ profile.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ profile.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 6
     $ project.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ project.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 4
     $ project.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ sample.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ sample.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 3
     $ sample.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ server.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ server.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options : Named list()
     $ validation.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ validation.template.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options : Named list()
     $ validation.data.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     $ status.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ status.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     ..$ options :List of 1
     > doc.MGRAST (3, stratum="parameters")
     List of 51
     $ annotation.info.parameters :List of 3
     ..$ body : Named list()
     ..$ options : Named list()
     ..$ required: Named list()
     $ annotation.sequence.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 7
     .. ..$ source :List of 2
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     .. ..$ type :List of 2
     .. ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ annotation.similarity.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 7
     .. ..$ source :List of 2
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     .. ..$ type :List of 2
     .. ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ compute.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ compute.alphadiversity.parameters:List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 2
     .. ..$ source:List of 2
     .. ..$ level :List of 2
     $ download.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ download.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
     ..$ options :List of 1
     .. ..$ file: chr [1:2] "string" "file name or identifier"
     $ download.setlist.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique metagenome identifier"
     ..$ options :List of 1
     .. ..$ stage: chr [1:2] "string" "stage name or identifier"
     $ inbox.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ inbox.view.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
     ..$ options : Named list()
     $ library.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ library.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 4
     .. ..$ verbosity:List of 2
     .. ..$ order :List of 2
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ library.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 1
     .. ..$ verbosity:List of 2
     $ m5nr.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ m5nr.ontology.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 6
     .. ..$ source :List of 2
     .. ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ filter : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
     .. ..$ exact : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
     .. ..$ filter_level:List of 2
     .. ..$ min_level :List of 2
     $ m5nr.taxonomy.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 5
     .. ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ filter : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
     .. ..$ exact : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
     .. ..$ filter_level:List of 2
     .. ..$ min_level :List of 2
     $ m5nr.sources.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 1
     .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     $ m5nr.accession.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique identifier from source DB"
     ..$ options :List of 4
     .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.alias.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ text: chr [1:2] "string" "text string of partial alias"
     ..$ options :List of 6
     .. ..$ source : chr [1:2] "string" "source name to restrict search by"
     .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.md5.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
     ..$ options :List of 7
     .. ..$ source : chr [1:2] "string" "source name to restrict search by"
     .. ..$ format :List of 2
     .. ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
     .. ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.function.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ text: chr [1:2] "string" "text string of partial function name"
     ..$ options :List of 7
     .. ..$ source : chr [1:2] "string" "source name to restrict search by"
     .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     .. ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     $ m5nr.organism.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ text: chr [1:2] "string" "text string of partial organism name"
     ..$ options :List of 8
     .. ..$ source : chr [1:2] "string" "source name to restrict search by"
     .. ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     .. ..$ inverse : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ tax_level:List of 2
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.sequence.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ text: chr [1:2] "string" "text string of protein sequence"
     ..$ options :List of 5
     .. ..$ source : chr [1:2] "string" "source name to restrict search by"
     .. ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     .. ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ matrix.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ matrix.organism.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 15
     .. ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     .. ..$ source :List of 2
     .. ..$ result_type :List of 2
     .. ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
     .. ..$ group_level :List of 2
     .. ..$ taxid : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
     .. ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ filter_source:List of 2
     .. ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     .. ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     .. ..$ filter_level :List of 2
     .. ..$ hit_type :List of 2
     $ matrix.function.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 13
     .. ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     .. ..$ source :List of 2
     .. ..$ result_type :List of 2
     .. ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     .. ..$ group_level :List of 2
     .. ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ filter_source:List of 2
     .. ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     .. ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     .. ..$ filter_level :List of 2
     $ matrix.feature.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 11
     .. ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     .. ..$ source :List of 2
     .. ..$ result_type :List of 2
     .. ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
     .. ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     .. ..$ hide_metadata : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     .. ..$ filter_level :List of 2
     $ metadata.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metadata.template.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metadata.cv.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 2
     .. ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
     .. ..$ label : chr [1:2] "string" "metadata label"
     ..$ required: Named list()
     $ metadata.ontology.parameters :List of 3
     ..$ body : Named list()
     ..$ options : Named list()
     ..$ required:List of 2
     .. ..$ version: chr [1:2] "string" "version of ontology to use"
     .. ..$ name : chr [1:2] "string" "ontology name"
     $ metadata.export.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options : Named list()
     $ metadata.validate.parameters :List of 3
     ..$ body : Named list()
     ..$ options :List of 5
     .. ..$ group :List of 2
     .. ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
     .. ..$ value : chr [1:2] "string" "metadata value"
     .. ..$ label : chr [1:2] "string" "metadata label"
     .. ..$ category:List of 2
     ..$ required: Named list()
     $ metagenome.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ metagenome.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 11
     .. ..$ verbosity:List of 2
     .. ..$ function : chr [1:2] "string" "search parameter: query string for function"
     .. ..$ status :List of 2
     .. ..$ match :List of 2
     .. ..$ direction:List of 2
     .. ..$ order : chr [1:2] "string" "metagenome object field to sort by (default is id)"
     .. ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ md5 : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
     .. ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ metagenome.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 1
     .. ..$ verbosity:List of 2
     $ profile.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ profile.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 6
     .. ..$ source :List of 2
     .. ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     .. ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     .. ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     .. ..$ type :List of 2
     .. ..$ hit_type:List of 2
     $ project.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ project.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 4
     .. ..$ verbosity:List of 2
     .. ..$ order :List of 2
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ project.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 1
     .. ..$ verbosity:List of 2
     $ sample.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ sample.query.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options :List of 3
     .. ..$ order :List of 2
     .. ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     .. ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ sample.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique object identifier"
     ..$ options :List of 1
     .. ..$ verbosity:List of 2
     $ server.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ server.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique server ID"
     ..$ options : Named list()
     $ validation.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ validation.template.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "SHOCK template id"
     ..$ options : Named list()
     $ validation.data.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "SHOCK data id"
     ..$ options :List of 1
     .. ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
     $ status.info.parameters :List of 3
     ..$ body : Named list()
     ..$ required: Named list()
     ..$ options : Named list()
     $ status.instance.parameters :List of 3
     ..$ body : Named list()
     ..$ required:List of 1
     .. ..$ id: chr [1:2] "string" "unique process id"
     ..$ options :List of 1
     .. ..$ verbosity:List of 2
     >
     > doc.MGRAST (stratum="options")
     List of 51
     $ annotation.info.parameters.options : Named list()
     $ annotation.sequence.parameters.options :List of 7
     $ annotation.similarity.parameters.options :List of 7
     $ compute.info.parameters.options : Named list()
     $ compute.alphadiversity.parameters.options:List of 2
     $ download.info.parameters.options : Named list()
     $ download.instance.parameters.options :List of 1
     $ download.setlist.parameters.options :List of 1
     $ inbox.info.parameters.options : Named list()
     $ inbox.view.parameters.options : Named list()
     $ library.info.parameters.options : Named list()
     $ library.query.parameters.options :List of 4
     $ library.instance.parameters.options :List of 1
     $ m5nr.info.parameters.options : Named list()
     $ m5nr.ontology.parameters.options :List of 6
     $ m5nr.taxonomy.parameters.options :List of 5
     $ m5nr.sources.parameters.options :List of 1
     $ m5nr.accession.parameters.options :List of 4
     $ m5nr.alias.parameters.options :List of 6
     $ m5nr.md5.parameters.options :List of 7
     $ m5nr.function.parameters.options :List of 7
     $ m5nr.organism.parameters.options :List of 8
     $ m5nr.sequence.parameters.options :List of 5
     $ matrix.info.parameters.options : Named list()
     $ matrix.organism.parameters.options :List of 15
     $ matrix.function.parameters.options :List of 13
     $ matrix.feature.parameters.options :List of 11
     $ metadata.info.parameters.options : Named list()
     $ metadata.template.parameters.options : Named list()
     $ metadata.cv.parameters.options :List of 2
     $ metadata.ontology.parameters.options : Named list()
     $ metadata.export.parameters.options : Named list()
     $ metadata.validate.parameters.options :List of 5
     $ metagenome.info.parameters.options : Named list()
     $ metagenome.query.parameters.options :List of 11
     $ metagenome.instance.parameters.options :List of 1
     $ profile.info.parameters.options : Named list()
     $ profile.instance.parameters.options :List of 6
     $ project.info.parameters.options : Named list()
     $ project.query.parameters.options :List of 4
     $ project.instance.parameters.options :List of 1
     $ sample.info.parameters.options : Named list()
     $ sample.query.parameters.options :List of 3
     $ sample.instance.parameters.options :List of 1
     $ server.info.parameters.options : Named list()
     $ server.instance.parameters.options : Named list()
     $ validation.info.parameters.options : Named list()
     $ validation.template.parameters.options : Named list()
     $ validation.data.parameters.options :List of 1
     $ status.info.parameters.options : Named list()
     $ status.instance.parameters.options :List of 1
     > doc.MGRAST (2, stratum="options")
     List of 51
     $ annotation.info.parameters.options : Named list()
     $ annotation.sequence.parameters.options :List of 7
     ..$ source :List of 2
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     ..$ type :List of 2
     ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     $ annotation.similarity.parameters.options :List of 7
     ..$ source :List of 2
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     ..$ type :List of 2
     ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     $ compute.info.parameters.options : Named list()
     $ compute.alphadiversity.parameters.options:List of 2
     ..$ source:List of 2
     ..$ level :List of 2
     $ download.info.parameters.options : Named list()
     $ download.instance.parameters.options :List of 1
     ..$ file: chr [1:2] "string" "file name or identifier"
     $ download.setlist.parameters.options :List of 1
     ..$ stage: chr [1:2] "string" "stage name or identifier"
     $ inbox.info.parameters.options : Named list()
     $ inbox.view.parameters.options : Named list()
     $ library.info.parameters.options : Named list()
     $ library.query.parameters.options :List of 4
     ..$ verbosity:List of 2
     ..$ order :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ library.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     $ m5nr.info.parameters.options : Named list()
     $ m5nr.ontology.parameters.options :List of 6
     ..$ source :List of 2
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ filter : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
     ..$ exact : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
     ..$ filter_level:List of 2
     ..$ min_level :List of 2
     $ m5nr.taxonomy.parameters.options :List of 5
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ filter : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
     ..$ exact : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
     ..$ filter_level:List of 2
     ..$ min_level :List of 2
     $ m5nr.sources.parameters.options :List of 1
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     $ m5nr.accession.parameters.options :List of 4
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.alias.parameters.options :List of 6
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.md5.parameters.options :List of 7
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ format :List of 2
     ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.function.parameters.options :List of 7
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     $ m5nr.organism.parameters.options :List of 8
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ inverse : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ tax_level:List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.sequence.parameters.options :List of 5
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ matrix.info.parameters.options : Named list()
     $ matrix.organism.parameters.options :List of 15
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     ..$ result_type :List of 2
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
     ..$ group_level :List of 2
     ..$ taxid : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
     ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ filter_source:List of 2
     ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ filter_level :List of 2
     ..$ hit_type :List of 2
     $ matrix.function.parameters.options :List of 13
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     ..$ result_type :List of 2
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     ..$ group_level :List of 2
     ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ filter_source:List of 2
     ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ filter_level :List of 2
     $ matrix.feature.parameters.options :List of 11
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     ..$ result_type :List of 2
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ hide_metadata : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ filter_level :List of 2
     $ metadata.info.parameters.options : Named list()
     $ metadata.template.parameters.options : Named list()
     $ metadata.cv.parameters.options :List of 2
     ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
     ..$ label : chr [1:2] "string" "metadata label"
     $ metadata.ontology.parameters.options : Named list()
     $ metadata.export.parameters.options : Named list()
     $ metadata.validate.parameters.options :List of 5
     ..$ group :List of 2
     ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
     ..$ value : chr [1:2] "string" "metadata value"
     ..$ label : chr [1:2] "string" "metadata label"
     ..$ category:List of 2
     $ metagenome.info.parameters.options : Named list()
     $ metagenome.query.parameters.options :List of 11
     ..$ verbosity:List of 2
     ..$ function : chr [1:2] "string" "search parameter: query string for function"
     ..$ status :List of 2
     ..$ match :List of 2
     ..$ direction:List of 2
     ..$ order : chr [1:2] "string" "metagenome object field to sort by (default is id)"
     ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ md5 : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
     ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ metagenome.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     $ profile.info.parameters.options : Named list()
     $ profile.instance.parameters.options :List of 6
     ..$ source :List of 2
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ type :List of 2
     ..$ hit_type:List of 2
     $ project.info.parameters.options : Named list()
     $ project.query.parameters.options :List of 4
     ..$ verbosity:List of 2
     ..$ order :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ project.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     $ sample.info.parameters.options : Named list()
     $ sample.query.parameters.options :List of 3
     ..$ order :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ sample.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     $ server.info.parameters.options : Named list()
     $ server.instance.parameters.options : Named list()
     $ validation.info.parameters.options : Named list()
     $ validation.template.parameters.options : Named list()
     $ validation.data.parameters.options :List of 1
     ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
     $ status.info.parameters.options : Named list()
     $ status.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     > doc.MGRAST (3, stratum="options")
     List of 51
     $ annotation.info.parameters.options : Named list()
     $ annotation.sequence.parameters.options :List of 7
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 16
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     ..$ type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 5
     ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     $ annotation.similarity.parameters.options :List of 7
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 16
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ filter : chr [1:2] "string" "text string to filter annotations by: only return those that contain text"
     ..$ type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 5
     ..$ filter_level: chr [1:2] "string" "hierarchal level to filter annotations by, for organism or ontology only"
     $ compute.info.parameters.options : Named list()
     $ compute.alphadiversity.parameters.options:List of 2
     ..$ source:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 12
     ..$ level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 8
     $ download.info.parameters.options : Named list()
     $ download.instance.parameters.options :List of 1
     ..$ file: chr [1:2] "string" "file name or identifier"
     $ download.setlist.parameters.options :List of 1
     ..$ stage: chr [1:2] "string" "stage name or identifier"
     $ inbox.info.parameters.options : Named list()
     $ inbox.view.parameters.options : Named list()
     $ library.info.parameters.options : Named list()
     $ library.query.parameters.options :List of 4
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 1
     ..$ order :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ library.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     $ m5nr.info.parameters.options : Named list()
     $ m5nr.ontology.parameters.options :List of 6
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ filter : chr [1:2] "string" "text of ontology group (filter_level) to filter by"
     ..$ exact : chr [1:2] "boolean" "if true return only those ontologies that exactly match filter, default is false"
     ..$ filter_level:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ min_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     $ m5nr.taxonomy.parameters.options :List of 5
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ filter : chr [1:2] "string" "text of taxanomy group (filter_level) to filter by"
     ..$ exact : chr [1:2] "boolean" "if true return only those taxonomies that exactly match filter, default is false"
     ..$ filter_level:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 7
     ..$ min_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 7
     $ m5nr.sources.parameters.options :List of 1
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     $ m5nr.accession.parameters.options :List of 4
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.alias.parameters.options :List of 6
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.md5.parameters.options :List of 7
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ format :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ sequence: chr [1:2] "boolean" "if true return sequence output, else return annotation output, default is false"
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.function.parameters.options :List of 7
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     ..$ inverse: chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     $ m5nr.organism.parameters.options :List of 8
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version : chr [1:2] "integer" "M5NR version, default 10"
     ..$ exact : chr [1:2] "boolean" "if true return only those annotations that exactly match input text, default is false"
     ..$ inverse : chr [1:2] "boolean" "if true return only those annotations that do not match input text, default is false"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ tax_level:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 8
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ m5nr.sequence.parameters.options :List of 5
     ..$ source : chr [1:2] "string" "source name to restrict search by"
     ..$ version: chr [1:2] "integer" "M5NR version, default 10"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ matrix.info.parameters.options : Named list()
     $ matrix.organism.parameters.options :List of 15
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 14
     ..$ result_type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this function"
     ..$ group_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 8
     ..$ taxid : chr [1:2] "boolean" "if true, return annotation ID as NCBI tax id. Only for group_levels with a tax_id"
     ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ filter_source:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ filter_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ hit_type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     $ matrix.function.parameters.options :List of 13
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ result_type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     ..$ group_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ grep : chr [1:2] "string" "filter the return results to only include annotations that contain this text"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ filter_source:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 14
     ..$ hide_metadata: chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ filter_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 8
     $ matrix.feature.parameters.options :List of 11
     ..$ asynchronous : chr [1:2] "boolean" "if true return process id to query status resource for results, default is false"
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 12
     ..$ result_type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     ..$ filter : chr [1:2] "string" "filter the return results to only include abundances based on genes with this organism"
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ identity : chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ hide_annotation: chr [1:2] "boolean" "if true do not return feature metadata in 'rows' object, default is false"
     ..$ id : chr [1:2] "string" "one or more metagenome or project unique identifier"
     ..$ hide_metadata : chr [1:2] "boolean" "if true do not return metagenome metadata in 'columns' object, default is false"
     ..$ filter_level :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 8
     $ metadata.info.parameters.options : Named list()
     $ metadata.template.parameters.options : Named list()
     $ metadata.cv.parameters.options :List of 2
     ..$ version: chr [1:2] "string" "version of CV select list or ontology to use"
     ..$ label : chr [1:2] "string" "metadata label"
     $ metadata.ontology.parameters.options : Named list()
     $ metadata.export.parameters.options : Named list()
     $ metadata.validate.parameters.options :List of 5
     ..$ group :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     ..$ version : chr [1:2] "string" "version of CV select list or ontology to use"
     ..$ value : chr [1:2] "string" "metadata value"
     ..$ label : chr [1:2] "string" "metadata label"
     ..$ category:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     $ metagenome.info.parameters.options : Named list()
     $ metagenome.query.parameters.options :List of 11
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 5
     ..$ function : chr [1:2] "string" "search parameter: query string for function"
     ..$ status :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     ..$ match :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ direction:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ order : chr [1:2] "string" "metagenome object field to sort by (default is id)"
     ..$ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ md5 : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
     ..$ organism : chr [1:2] "string" "search parameter: query string for organism"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ metagenome.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 4
     $ profile.info.parameters.options : Named list()
     $ profile.instance.parameters.options :List of 6
     ..$ source :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 18
     ..$ length : chr [1:2] "int" "value for minimum alignment length cutoff: default is 15"
     ..$ identity: chr [1:2] "int" "percent value for minimum % identity cutoff: default is 60"
     ..$ evalue : chr [1:2] "int" "negative exponent value for maximum e-value cutoff: default is 5"
     ..$ type :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     ..$ hit_type:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     $ project.info.parameters.options : Named list()
     $ project.query.parameters.options :List of 4
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     ..$ order :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset : chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ project.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     $ sample.info.parameters.options : Named list()
     $ sample.query.parameters.options :List of 3
     ..$ order :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ limit : chr [1:2] "integer" "maximum number of items requested"
     ..$ offset: chr [1:2] "integer" "zero based index of the first data object to be returned"
     $ sample.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 3
     $ server.info.parameters.options : Named list()
     $ server.instance.parameters.options : Named list()
     $ validation.info.parameters.options : Named list()
     $ validation.template.parameters.options : Named list()
     $ validation.data.parameters.options :List of 1
     ..$ template: chr [1:2] "string" "SHOCK template id, default is MG-RAST metagenome metadata template"
     $ status.info.parameters.options : Named list()
     $ status.instance.parameters.options :List of 1
     ..$ verbosity:List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     >
     > doc.MGRAST (stratum="required")
     List of 51
     $ annotation.info.parameters.required : Named list()
     $ annotation.sequence.parameters.required :List of 1
     $ annotation.similarity.parameters.required :List of 1
     $ compute.info.parameters.required : Named list()
     $ compute.alphadiversity.parameters.required:List of 1
     $ download.info.parameters.required : Named list()
     $ download.instance.parameters.required :List of 1
     $ download.setlist.parameters.required :List of 1
     $ inbox.info.parameters.required : Named list()
     $ inbox.view.parameters.required :List of 1
     $ library.info.parameters.required : Named list()
     $ library.query.parameters.required : Named list()
     $ library.instance.parameters.required :List of 1
     $ m5nr.info.parameters.required : Named list()
     $ m5nr.ontology.parameters.required : Named list()
     $ m5nr.taxonomy.parameters.required : Named list()
     $ m5nr.sources.parameters.required : Named list()
     $ m5nr.accession.parameters.required :List of 1
     $ m5nr.alias.parameters.required :List of 1
     $ m5nr.md5.parameters.required :List of 1
     $ m5nr.function.parameters.required :List of 1
     $ m5nr.organism.parameters.required :List of 1
     $ m5nr.sequence.parameters.required :List of 1
     $ matrix.info.parameters.required : Named list()
     $ matrix.organism.parameters.required : Named list()
     $ matrix.function.parameters.required : Named list()
     $ matrix.feature.parameters.required : Named list()
     $ metadata.info.parameters.required : Named list()
     $ metadata.template.parameters.required : Named list()
     $ metadata.cv.parameters.required : Named list()
     $ metadata.ontology.parameters.required :List of 2
     $ metadata.export.parameters.required :List of 1
     $ metadata.validate.parameters.required : Named list()
     $ metagenome.info.parameters.required : Named list()
     $ metagenome.query.parameters.required : Named list()
     $ metagenome.instance.parameters.required :List of 1
     $ profile.info.parameters.required : Named list()
     $ profile.instance.parameters.required :List of 1
     $ project.info.parameters.required : Named list()
     $ project.query.parameters.required : Named list()
     $ project.instance.parameters.required :List of 1
     $ sample.info.parameters.required : Named list()
     $ sample.query.parameters.required : Named list()
     $ sample.instance.parameters.required :List of 1
     $ server.info.parameters.required : Named list()
     $ server.instance.parameters.required :List of 1
     $ validation.info.parameters.required : Named list()
     $ validation.template.parameters.required :List of 1
     $ validation.data.parameters.required :List of 1
     $ status.info.parameters.required : Named list()
     $ status.instance.parameters.required :List of 1
     > doc.MGRAST (2, stratum="required")
     List of 51
     $ annotation.info.parameters.required : Named list()
     $ annotation.sequence.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ annotation.similarity.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ compute.info.parameters.required : Named list()
     $ compute.alphadiversity.parameters.required:List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ download.info.parameters.required : Named list()
     $ download.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ download.setlist.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ inbox.info.parameters.required : Named list()
     $ inbox.view.parameters.required :List of 1
     ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
     $ library.info.parameters.required : Named list()
     $ library.query.parameters.required : Named list()
     $ library.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ m5nr.info.parameters.required : Named list()
     $ m5nr.ontology.parameters.required : Named list()
     $ m5nr.taxonomy.parameters.required : Named list()
     $ m5nr.sources.parameters.required : Named list()
     $ m5nr.accession.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique identifier from source DB"
     $ m5nr.alias.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial alias"
     $ m5nr.md5.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
     $ m5nr.function.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial function name"
     $ m5nr.organism.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial organism name"
     $ m5nr.sequence.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of protein sequence"
     $ matrix.info.parameters.required : Named list()
     $ matrix.organism.parameters.required : Named list()
     $ matrix.function.parameters.required : Named list()
     $ matrix.feature.parameters.required : Named list()
     $ metadata.info.parameters.required : Named list()
     $ metadata.template.parameters.required : Named list()
     $ metadata.cv.parameters.required : Named list()
     $ metadata.ontology.parameters.required :List of 2
     ..$ version: chr [1:2] "string" "version of ontology to use"
     ..$ name : chr [1:2] "string" "ontology name"
     $ metadata.export.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ metadata.validate.parameters.required : Named list()
     $ metagenome.info.parameters.required : Named list()
     $ metagenome.query.parameters.required : Named list()
     $ metagenome.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ profile.info.parameters.required : Named list()
     $ profile.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ project.info.parameters.required : Named list()
     $ project.query.parameters.required : Named list()
     $ project.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ sample.info.parameters.required : Named list()
     $ sample.query.parameters.required : Named list()
     $ sample.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ server.info.parameters.required : Named list()
     $ server.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique server ID"
     $ validation.info.parameters.required : Named list()
     $ validation.template.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "SHOCK template id"
     $ validation.data.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "SHOCK data id"
     $ status.info.parameters.required : Named list()
     $ status.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique process id"
     > doc.MGRAST (3, stratum="required")
     List of 51
     $ annotation.info.parameters.required : Named list()
     $ annotation.sequence.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ annotation.similarity.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ compute.info.parameters.required : Named list()
     $ compute.alphadiversity.parameters.required:List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ download.info.parameters.required : Named list()
     $ download.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ download.setlist.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique metagenome identifier"
     $ inbox.info.parameters.required : Named list()
     $ inbox.view.parameters.required :List of 1
     ..$ auth: chr [1:2] "string" "unique string of text generated by MG-RAST for your account"
     $ library.info.parameters.required : Named list()
     $ library.query.parameters.required : Named list()
     $ library.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ m5nr.info.parameters.required : Named list()
     $ m5nr.ontology.parameters.required : Named list()
     $ m5nr.taxonomy.parameters.required : Named list()
     $ m5nr.sources.parameters.required : Named list()
     $ m5nr.accession.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique identifier from source DB"
     $ m5nr.alias.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial alias"
     $ m5nr.md5.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique identifier in form of md5 checksum"
     $ m5nr.function.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial function name"
     $ m5nr.organism.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of partial organism name"
     $ m5nr.sequence.parameters.required :List of 1
     ..$ text: chr [1:2] "string" "text string of protein sequence"
     $ matrix.info.parameters.required : Named list()
     $ matrix.organism.parameters.required : Named list()
     $ matrix.function.parameters.required : Named list()
     $ matrix.feature.parameters.required : Named list()
     $ metadata.info.parameters.required : Named list()
     $ metadata.template.parameters.required : Named list()
     $ metadata.cv.parameters.required : Named list()
     $ metadata.ontology.parameters.required :List of 2
     ..$ version: chr [1:2] "string" "version of ontology to use"
     ..$ name : chr [1:2] "string" "ontology name"
     $ metadata.export.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ metadata.validate.parameters.required : Named list()
     $ metagenome.info.parameters.required : Named list()
     $ metagenome.query.parameters.required : Named list()
     $ metagenome.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ profile.info.parameters.required : Named list()
     $ profile.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ project.info.parameters.required : Named list()
     $ project.query.parameters.required : Named list()
     $ project.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ sample.info.parameters.required : Named list()
     $ sample.query.parameters.required : Named list()
     $ sample.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique object identifier"
     $ server.info.parameters.required : Named list()
     $ server.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique server ID"
     $ validation.info.parameters.required : Named list()
     $ validation.template.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "SHOCK template id"
     $ validation.data.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "SHOCK data id"
     $ status.info.parameters.required : Named list()
     $ status.instance.parameters.required :List of 1
     ..$ id: chr [1:2] "string" "unique process id"
     >
     > doc.MGRAST (stratum="attributes")
     List of 51
     $ annotation.info.attributes : chr "self"
     $ annotation.sequence.attributes :List of 1
     $ annotation.similarity.attributes :List of 1
     $ compute.info.attributes : chr "self"
     $ compute.alphadiversity.attributes:List of 3
     $ download.info.attributes : chr "self"
     $ download.instance.attributes :List of 1
     $ download.setlist.attributes :List of 7
     $ inbox.info.attributes : chr "self"
     $ inbox.view.attributes :List of 4
     $ library.info.attributes : chr "self"
     $ library.query.attributes :List of 7
     $ library.instance.attributes :List of 10
     $ m5nr.info.attributes : chr "self"
     $ m5nr.ontology.attributes :List of 3
     $ m5nr.taxonomy.attributes :List of 3
     $ m5nr.sources.attributes :List of 3
     $ m5nr.accession.attributes :List of 8
     $ m5nr.alias.attributes :List of 8
     $ m5nr.md5.attributes :List of 8
     $ m5nr.function.attributes :List of 8
     $ m5nr.organism.attributes :List of 8
     $ m5nr.sequence.attributes :List of 8
     $ matrix.info.attributes : chr "self"
     $ matrix.organism.attributes :List of 14
     $ matrix.function.attributes :List of 14
     $ matrix.feature.attributes :List of 14
     $ metadata.info.attributes : chr "self"
     $ metadata.template.attributes :List of 4
     $ metadata.cv.attributes :List of 3
     $ metadata.ontology.attributes :List of 6
     $ metadata.export.attributes :List of 5
     $ metadata.validate.attributes :List of 2
     $ metagenome.info.attributes : chr "self"
     $ metagenome.query.attributes :List of 9
     $ metagenome.instance.attributes :List of 13
     $ profile.info.attributes : chr "self"
     $ profile.instance.attributes :List of 12
     $ project.info.attributes : chr "self"
     $ project.query.attributes :List of 7
     $ project.instance.attributes :List of 13
     $ sample.info.attributes : chr "self"
     $ sample.query.attributes :List of 7
     $ sample.instance.attributes :List of 10
     $ server.info.attributes : chr "self"
     $ server.instance.attributes :List of 9
     $ validation.info.attributes : chr "self"
     $ validation.template.attributes :List of 2
     $ validation.data.attributes :List of 2
     $ status.info.attributes : chr "self"
     $ status.instance.attributes :List of 4
     > doc.MGRAST (2, stratum="attributes")
     List of 51
     $ annotation.info.attributes : chr "self"
     $ annotation.sequence.attributes :List of 1
     ..$ streaming text:List of 2
     $ annotation.similarity.attributes :List of 1
     ..$ streaming text:List of 2
     $ compute.info.attributes : chr "self"
     $ compute.alphadiversity.attributes:List of 3
     ..$ url : chr [1:2] "string" "resource location of this object instance"
     ..$ data: chr [1:2] "float" "alpha diversity value"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     $ download.info.attributes : chr "self"
     $ download.instance.attributes :List of 1
     ..$ data: chr [1:2] "file" "requested analysis file"
     $ download.setlist.attributes :List of 7
     ..$ stage_name: chr [1:2] "string" "name of the stage in processing of this file"
     ..$ file_name : chr [1:2] "string" "name of the analysis file"
     ..$ url : chr [1:2] "string" "url for retrieving this analysis file"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     ..$ file_id : chr [1:2] "string" "unique identifier of file in stage"
     ..$ stage_type: chr [1:2] "string" "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
     ..$ stage_id : chr [1:2] "string" "three digit numerical identifier of the stage"
     $ inbox.info.attributes : chr "self"
     $ inbox.view.attributes :List of 4
     ..$ timestamp: chr [1:2] "string" "timestamp for return of this query"
     ..$ files :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "user login"
     $ library.info.attributes : chr "self"
     $ library.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ library.instance.attributes :List of 10
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ project : chr [1:2] "reference project" "reference to the project object"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ sequencesets:List of 2
     ..$ metagenome : chr [1:2] "reference metagenome" "reference to the related metagenome object"
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ sample : chr [1:2] "reference sample" "reference to the related sample object"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     $ m5nr.info.attributes : chr "self"
     $ m5nr.ontology.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     $ m5nr.taxonomy.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     $ m5nr.sources.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     $ m5nr.accession.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.alias.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.md5.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.function.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.organism.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.sequence.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ matrix.info.attributes : chr "self"
     $ matrix.organism.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     ..$ rows :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ matrix.function.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     ..$ rows :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ matrix.feature.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     ..$ rows :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ metadata.info.attributes : chr "self"
     $ metadata.template.attributes :List of 4
     ..$ ep :List of 2
     ..$ project:List of 2
     ..$ library:List of 2
     ..$ sample :List of 2
     $ metadata.cv.attributes :List of 3
     ..$ ontology:List of 2
     ..$ ont_info:List of 2
     ..$ select :List of 2
     $ metadata.ontology.attributes :List of 6
     ..$ version : chr [1:2] "string" "version of this ontology"
     ..$ rootNode: chr [1:2] "string" "ontology ID of root"
     ..$ name : chr [1:2] "string" "ontology name"
     ..$ type : chr [1:2] "string" "this type"
     ..$ showRoot: chr [1:2] "boolean" "option to show root when displaying"
     ..$ nodes :List of 2
     $ metadata.export.attributes :List of 5
     ..$ sampleNum: chr [1:2] "int" "number of samples in project"
     ..$ samples :List of 2
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ data :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     $ metadata.validate.attributes :List of 2
     ..$ message : chr [1:2] "string" "if not valid, reason why"
     ..$ is_valid: chr [1:2] "boolean" "the inputed value is valid for the given category and label"
     $ metagenome.info.attributes : chr "self"
     $ metagenome.query.attributes :List of 9
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ data :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ metagenome.instance.attributes :List of 13
     ..$ statistics : chr [1:2] "hash" "key value pairs describing statistics"
     ..$ status :List of 2
     ..$ version : chr [1:2] "integer" "version of the metagenome"
     ..$ project : chr [1:2] "reference project" "reference to the project object"
     ..$ name : chr [1:2] "string" "name of metagenome"
     ..$ sequence_type: chr [1:2] "string" "sequencing type"
     ..$ library : chr [1:2] "reference library" "reference to the related library object"
     ..$ created : chr [1:2] "date" "time the metagenome was first created"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     ..$ sample : chr [1:2] "reference sample" "reference to the related sample object"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing all metadata"
     ..$ mixs : chr [1:2] "hash" "key value pairs describing MIxS metadata"
     $ profile.info.attributes : chr "self"
     $ profile.instance.attributes :List of 12
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     ..$ rows :List of 2
     ..$ matrix_element_type: chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     ..$ shape :List of 2
     $ project.info.attributes : chr "self"
     $ project.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ project.instance.attributes :List of 13
     ..$ status :List of 2
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ description : chr [1:2] "string" "a short, comprehensive description of the project"
     ..$ metagenomes :List of 2
     ..$ libraries :List of 2
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ samples :List of 2
     ..$ funding_source: chr [1:2] "string" "the official name of the source of funding of this project"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ pi : chr [1:2] "string" "the first and last name of the principal investigator of the project"
     $ sample.info.attributes : chr "self"
     $ sample.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ sample.instance.attributes :List of 10
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ project : chr [1:2] "reference project" "reference to the project of this sample"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ metagenomes:List of 2
     ..$ libraries :List of 2
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ env_package:List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     $ server.info.attributes : chr "self"
     $ server.instance.attributes :List of 9
     ..$ info : chr [1:2] "string" "informational text, i.e. downtime warnings"
     ..$ basepairs : chr [1:2] "integer" "total number of basepairs"
     ..$ status : chr [1:2] "string" "status of the server"
     ..$ version : chr [1:2] "string" "version number of the server"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique identifier of this server"
     ..$ public_metagenomes: chr [1:2] "integer" "total number of public metagenomes"
     ..$ metagenomes : chr [1:2] "integer" "total number of metagenomes"
     ..$ sequences : chr [1:2] "integer" "total number of sequences"
     $ validation.info.attributes : chr "self"
     $ validation.template.attributes :List of 2
     ..$ error:List of 2
     ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
     $ validation.data.attributes :List of 2
     ..$ error:List of 2
     ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
     $ status.info.attributes : chr "self"
     $ status.instance.attributes :List of 4
     ..$ status:List of 3
     ..$ url : chr [1:2] "url" "resource location of this object instance"
     ..$ data : chr [1:2] "hash" "if status is done, data holds the result, otherwise data is not present"
     ..$ id : chr [1:2] "integer" "process id"
     > doc.MGRAST (3, stratum="attributes")
     List of 51
     $ annotation.info.attributes : chr "self"
     $ annotation.sequence.attributes :List of 1
     ..$ streaming text:List of 2
     .. ..$ : chr "object"
     .. ..$ :List of 2
     $ annotation.similarity.attributes :List of 1
     ..$ streaming text:List of 2
     .. ..$ : chr "object"
     .. ..$ :List of 2
     $ compute.info.attributes : chr "self"
     $ compute.alphadiversity.attributes:List of 3
     ..$ url : chr [1:2] "string" "resource location of this object instance"
     ..$ data: chr [1:2] "float" "alpha diversity value"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     $ download.info.attributes : chr "self"
     $ download.instance.attributes :List of 1
     ..$ data: chr [1:2] "file" "requested analysis file"
     $ download.setlist.attributes :List of 7
     ..$ stage_name: chr [1:2] "string" "name of the stage in processing of this file"
     ..$ file_name : chr [1:2] "string" "name of the analysis file"
     ..$ url : chr [1:2] "string" "url for retrieving this analysis file"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     ..$ file_id : chr [1:2] "string" "unique identifier of file in stage"
     ..$ stage_type: chr [1:2] "string" "type of the analysis file within a stage, i.e. passed or removed for quality control steps"
     ..$ stage_id : chr [1:2] "string" "three digit numerical identifier of the stage"
     $ inbox.info.attributes : chr "self"
     $ inbox.view.attributes :List of 4
     ..$ timestamp: chr [1:2] "string" "timestamp for return of this query"
     ..$ files :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "user login"
     $ library.info.attributes : chr "self"
     $ library.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ library.instance.attributes :List of 10
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ project : chr [1:2] "reference project" "reference to the project object"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ sequencesets:List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference sequenceset" "a list of references to the related sequence sets"
     ..$ metagenome : chr [1:2] "reference metagenome" "reference to the related metagenome object"
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ sample : chr [1:2] "reference sample" "reference to the related sample object"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     $ m5nr.info.attributes : chr "self"
     $ m5nr.ontology.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     $ m5nr.taxonomy.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     $ m5nr.sources.attributes :List of 3
     ..$ version: chr [1:2] "integer" "version of M5NR"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "object" "source object"
     $ m5nr.accession.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.alias.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.md5.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.function.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.organism.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ m5nr.sequence.attributes :List of 8
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of M5NR"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ matrix.info.attributes : chr "self"
     $ matrix.organism.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ rows :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ matrix.function.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ rows :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ matrix.feature.attributes :List of 14
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ rows :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ matrix_element_value: chr [1:2] "string" "result_type of the elements in the return matrix"
     ..$ matrix_element_type : chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ shape :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     $ metadata.info.attributes : chr "self"
     $ metadata.template.attributes :List of 4
     ..$ ep :List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ project:List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ library:List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ sample :List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     $ metadata.cv.attributes :List of 3
     ..$ ontology:List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ ont_info:List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ select :List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     $ metadata.ontology.attributes :List of 6
     ..$ version : chr [1:2] "string" "version of this ontology"
     ..$ rootNode: chr [1:2] "string" "ontology ID of root"
     ..$ name : chr [1:2] "string" "ontology name"
     ..$ type : chr [1:2] "string" "this type"
     ..$ showRoot: chr [1:2] "boolean" "option to show root when displaying"
     ..$ nodes :List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     $ metadata.export.attributes :List of 5
     ..$ sampleNum: chr [1:2] "int" "number of samples in project"
     ..$ samples :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "object" "sample object containing sample metadata, sample libraries, sample envPackage"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ data :List of 2
     .. ..$ : chr "hash"
     .. ..$ :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     $ metadata.validate.attributes :List of 2
     ..$ message : chr [1:2] "string" "if not valid, reason why"
     ..$ is_valid: chr [1:2] "boolean" "the inputed value is valid for the given category and label"
     $ metagenome.info.attributes : chr "self"
     $ metagenome.query.attributes :List of 9
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     $ metagenome.instance.attributes :List of 13
     ..$ statistics : chr [1:2] "hash" "key value pairs describing statistics"
     ..$ status :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ version : chr [1:2] "integer" "version of the metagenome"
     ..$ project : chr [1:2] "reference project" "reference to the project object"
     ..$ name : chr [1:2] "string" "name of metagenome"
     ..$ sequence_type: chr [1:2] "string" "sequencing type"
     ..$ library : chr [1:2] "reference library" "reference to the related library object"
     ..$ created : chr [1:2] "date" "time the metagenome was first created"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique metagenome identifier"
     ..$ sample : chr [1:2] "reference sample" "reference to the related sample object"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing all metadata"
     ..$ mixs : chr [1:2] "hash" "key value pairs describing MIxS metadata"
     $ profile.info.attributes : chr "self"
     $ profile.instance.attributes :List of 12
     ..$ generated_by : chr [1:2] "string" "identifier of the data generator"
     ..$ matrix_type : chr [1:2] "string" "type of the data encoding matrix (dense or sparse)"
     ..$ date : chr [1:2] "date" "time the output data was generated"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ rows :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ matrix_element_type: chr [1:2] "string" "data type of the elements in the return matrix"
     ..$ format_url : chr [1:2] "string" "url to the format specification"
     ..$ format : chr [1:2] "string" "format specification name"
     ..$ columns :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ type : chr [1:2] "string" "type of the data in the return table (taxon, function or gene)"
     ..$ shape :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "integer" "list of the dimension sizes of the return matrix"
     $ project.info.attributes : chr "self"
     $ project.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ project.instance.attributes :List of 13
     ..$ status :List of 2
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ description : chr [1:2] "string" "a short, comprehensive description of the project"
     ..$ metagenomes :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference metagenome" "a list of references to the related metagenome objects"
     ..$ libraries :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference library" "a list of references to the related library objects"
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ samples :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference sample" "a list of references to the related sample objects"
     ..$ funding_source: chr [1:2] "string" "the official name of the source of funding of this project"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ pi : chr [1:2] "string" "the first and last name of the principal investigator of the project"
     $ sample.info.attributes : chr "self"
     $ sample.query.attributes :List of 7
     ..$ next : chr [1:2] "uri" "link to the previous set or null if this is the first set"
     ..$ prev : chr [1:2] "uri" "link to the next set or null if this is the last set"
     ..$ order : chr [1:2] "string" "name of the attribute the returned data is ordered by"
     ..$ limit : chr [1:2] "integer" "maximum number of data items returned, default is 10"
     ..$ data :List of 2
     .. ..$ : chr "list"
     .. ..$ :List of 2
     ..$ offset : chr [1:2] "integer" "zero based index of the first returned data item"
     ..$ total_count: chr [1:2] "integer" "total number of available data items"
     $ sample.instance.attributes :List of 10
     ..$ version : chr [1:2] "integer" "version of the object"
     ..$ project : chr [1:2] "reference project" "reference to the project of this sample"
     ..$ name : chr [1:2] "string" "human readable identifier"
     ..$ metagenomes:List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference metagenome" "a list of references to the related metagenome objects"
     ..$ libraries :List of 2
     .. ..$ : chr "list"
     .. ..$ : chr [1:2] "reference library" "a list of references to the related library objects"
     ..$ created : chr [1:2] "date" "time the object was first created"
     ..$ env_package:List of 2
     .. ..$ : chr "object"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique object identifier"
     ..$ metadata : chr [1:2] "hash" "key value pairs describing metadata"
     $ server.info.attributes : chr "self"
     $ server.instance.attributes :List of 9
     ..$ info : chr [1:2] "string" "informational text, i.e. downtime warnings"
     ..$ basepairs : chr [1:2] "integer" "total number of basepairs"
     ..$ status : chr [1:2] "string" "status of the server"
     ..$ version : chr [1:2] "string" "version number of the server"
     ..$ url : chr [1:2] "uri" "resource location of this object instance"
     ..$ id : chr [1:2] "string" "unique identifier of this server"
     ..$ public_metagenomes: chr [1:2] "integer" "total number of public metagenomes"
     ..$ metagenomes : chr [1:2] "integer" "total number of metagenomes"
     ..$ sequences : chr [1:2] "integer" "total number of sequences"
     $ validation.info.attributes : chr "self"
     $ validation.template.attributes :List of 2
     ..$ error:List of 2
     .. ..$ : chr "array"
     .. ..$ : chr [1:2] "string" "array of invalid entries"
     ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
     $ validation.data.attributes :List of 2
     ..$ error:List of 2
     .. ..$ : chr "array"
     .. ..$ : chr [1:2] "string" "array of invalid entries"
     ..$ valid: chr [1:2] "boolean" "boolean indicating whether the examined template is valid or not"
     $ status.info.attributes : chr "self"
     $ status.instance.attributes :List of 4
     ..$ status:List of 3
     .. ..$ : chr "string"
     .. ..$ : chr "cv"
     .. ..$ :List of 2
     ..$ url : chr [1:2] "url" "resource location of this object instance"
     ..$ data : chr [1:2] "hash" "if status is done, data holds the result, otherwise data is not present"
     ..$ id : chr [1:2] "integer" "process id"
     >
     > doc.MGRAST (2, head = c('mat','orga','param','opt','group_level'))
     List of 2
     $ : chr "cv"
     $ :List of 8
     ..$ : chr [1:2] "strain" "bottom organism taxanomic level"
     ..$ : chr [1:2] "species" "organism type level"
     ..$ : chr [1:2] "genus" "organism taxanomic level"
     ..$ : chr [1:2] "family" "organism taxanomic level"
     ..$ : chr [1:2] "order" "organism taxanomic level"
     ..$ : chr [1:2] "class" "organism taxanomic level"
     ..$ : chr [1:2] "phylum" "organism taxanomic level"
     ..$ : chr [1:2] "domain" "top organism taxanomic level"
     > doc.MGRAST (2, head = c('mat','func','param','opt','group_level'))
     List of 2
     $ : chr "cv"
     $ :List of 4
     ..$ : chr [1:2] "function" "bottom function ontology level"
     ..$ : chr [1:2] "level3" "function ontology level"
     ..$ : chr [1:2] "level2" "function ontology level"
     ..$ : chr [1:2] "level1" "top function ontology level"
     >
     > #-----------------------------------------------------------------------------
     > # test URL construction from arguments, without issuing any calls.
     > #
     > # the first set are calls from API documentation, adapted by hand, April 2014.
     > # some are copied in the doc examples of call.MGRAST() and parse.MGRAST().
     > # if these are updated, so should those be. (see above for the original URLs.)
     > #
     > # the second set are test cases put together by hand.
     > # calls intended to produce errors are "try"d.
     > #-----------------------------------------------------------------------------
     >
     > call.MGRAST ('an', 'se', id=4447943.3, ev=10, ty='or', so='Sw', destfile="no.file", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
     > call.MGRAST ('an', 'si', id=4447943.3, iden=80, ty='fu', so='KO', destfile="no.file", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO"
     > call.MGRAST ('co', 'al', id=4447943.3, le='or', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/compute/alphadiversity/mgm4447943.3?level=order"
     > call.MGRAST ('do', 'ins', id=4447943.3, fi=350.1, destfile="no.file", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/download/mgm4447943.3?file=350.1"
     > call.MGRAST ('do', 'se', id=4447943.3, st=650, issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/download/mgm4447943.3?stage=650"
     > call.MGRAST ('li', 'qu', li=20, or='na', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/library?limit=20&order=name"
     > call.MGRAST ('li', 'ins', id=52924, ve='fu', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/library/mgl52924?verbosity=full"
     > call.MGRAST ('m5', 'on', so='Subsystems', mi='level3', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/ontology?source=Subsystems&min_level=level3"
     > call.MGRAST ('m5', 'ta', filter='Bacteroidetes', filter_l='phylum', mi='genus', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus"
     > call.MGRAST ('m5', 'so', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/sources"
     > call.MGRAST ('m5', 'ac', id='YP_003268079.1', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/accession/YP_003268079.1"
     > call.MGRAST ('m5', 'al', text='IPR001478', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/alias/IPR001478"
     > call.MGRAST ('m5', 'md', id='000821a2e2f63df1a3873e4b280002a8', so='InterPro', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro"
     > call.MGRAST ('m5', 'fu', text='sulfatase', so='GenBank', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/function/sulfatase?source=GenBank"
     > call.MGRAST ('m5', 'or', text='akkermansia', so='KEGG', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/organism/akkermansia?source=KEGG"
     > call.MGRAST ('m5', 'se', text='MAGENHQWQGSIL', so='TrEMBL', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/m5nr/sequence/MAGENHQWQGSIL?source=TrEMBL"
     > call.MGRAST ('ma', 'or', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), gro='family', so='Ref', resu='ab', ev=15, issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=family&source=RefSeq&result_type=abundance&evalue=15"
     > call.MGRAST ('ma', 'fu', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), gro='level3', so='Sub', resu='ab', iden=80, filter_l='phylum', filter='Firmicutes', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&group_level=level3&source=Subsystems&result_type=abundance&identity=80&filter_level=phylum&filter=Firmicutes"
     > call.MGRAST ('ma', 'fe', id=c(4447943.3, 4447192.3, 4447102.3, 4447103.3), so='KE', resu='ev', len=25, issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/matrix/feature?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&id=mgm4447103.3&source=KEGG&result_type=evalue&length=25"
     > call.MGRAST ('metadata', 'te', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/metadata/template"
     > call.MGRAST ('metadata', 'cv', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/metadata/cv"
     > call.MGRAST ('metadata', 'ex', id=128, issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/metadata/export/128"
     > call.MGRAST ('metageno','qu', li=20, ord='name', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/metagenome?limit=20&order=name"
     > call.MGRAST ('metageno','ins', id=4447943.3, ve='me', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/metagenome/mgm4447943.3?verbosity=metadata"
     > call.MGRAST ('proj', 'qu', li=20, or='na', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/project?limit=20&order=name"
     > call.MGRAST ('proj', 'ins', id=128, ve='fu', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/project/mgp128?verbosity=full"
     > call.MGRAST ('sa', 'qu', li=20, or='na', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/sample?limit=20&order=name"
     > call.MGRAST ('sa', 'ins', id=25823, ve='fu', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/sample/mgs25823?verbosity=full"
     > call.MGRAST ('va', 'te', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/validation/template"
     > call.MGRAST ('va', 'da', issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/validation/data"
     >
     > try (call.MGRAST ("ann", issue=FALSE))
     Error in match.arg(request, names(api.root[[resource]])) :
     argument "request" is missing, with no default
     > try (call.MGRAST ("ann", "seque", issue=FALSE))
     Error in call.MGRAST("ann", "seque", issue = FALSE) :
     an output file should be specified for this request
     > call.MGRAST ("ann", "seque", destfile="no.file", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/annotation/sequence"
     > call.MGRAST ("compu", "alpha", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/compute/alphadiversity"
     > call.MGRAST ("downloa", "setl", issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/download"
     > call.MGRAST ("downloa", "setl", id=5, issue=FALSE)
     [1] "http://api.metagenomics.anl.gov/1/download/mgm5"
     > try (call.MGRAST ("downloa", "sel", id=5, issue=FALSE))
     Error in match.arg(request, names(api.root[[resource]])) :
     'arg' should be one of "info", "instance", "setlist"
     > call.MGRAST ("download", "setlist", st=5, id=10, i=11, issue=FALSE)
     Error in length(required.str) && nchar(required.str) :
     'length = 2' in coercion to 'logical(1)'
     Calls: call.MGRAST -> paste
     Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc