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 |
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