Package: cosmosid-cli
CosmosID-HUB Microbiome CLICommand line interface (CLI) and Python 3 client library for interacting with the CosmosID-HUB API. Only works with
Python [3.6,3.7,3.8,3.9,3.10].RequirementsOS Packagespython3python3-pipPython packagepoetryInstallationThis package provides:core Python 3 client library;a simple CLI for interacting with the CosmosID-HUB API;Basic installationThe CLI with the core Python library can be installed usingpip3.simply run from consolesudo pip3 install cosmosid_cliNote: pip3 and setuptools should be upgraded to latest version. Please update those packages on you workstation
regarding to your OS update process before setup CosmosID-HUB CLI.E.g.forUbuntu14.04performfollowingsteps:
$sudoapt-getupdate
$sudoapt-getupgrade
$sudo-Hpip3install-UpipsetuptoolsIf you had have previously installed CosmosID-HUB CLI just upgrade CLI
to latest version.$sudo-Hpip3install--upgradecosmosid_cliTo install package locally from folder with source files do the following:installpoetrycheck thedoccd cosmosid-cli/package/poetry installInstallation from package management service Anaconda.orgAssure that you have Conda already installed or install it based on your system requirements -linkFollow thecosmosid project pageto check the last version of cosmosid-cli available on Anaconda.orgThe CLI with Conda can be installed by the following command:condainstall-ccosmosid-cconda-forgecosmosid-cliVerify the CLI version installedcosmosid--versionUsing the CosmosID-HUB CLIThe CosmosID-HUB CLI supports authentication via CosmosID-HUB API Key.
Your API key can be found on theCosmosID-HUB profile page.
To automatically authenticate via CosmosID-HUB API Key you should create
credential file~/.cosmosidand store your API Key into it in
the following format:{"api_key":"<your api key string>"}You can directly use your CosmosID-HUB API Key, rather than storing it in a credential file. To use API Key authentication,
pass your key as an argument to thecosmosidcommand:cosmosid--api_key=YOUR_API_KEY<command>CLI supports files of following extensions: 'fasta', 'fna', 'fasta.gz', 'fastq', 'fq', 'fastq.gz', 'bam', 'sra'CommandsThere are several types of commands supported by the CosmosID-HUB CLICommands for retrieving data to terminal (output) from CosmosID cloud - files, runs, analysis.Commands for uploading metagenomics or amplicon samples to
CosmosID cloud for analysis - uploads.Commands for retrieving the reports archive from CosmosID cloud - reportsNote: Each command has options. To get usage information for each CosmosID-HUB CLI command, the user can simply
runcosmosid <command> --helpRetrieve FilesThe commands for retrieving data have options for output format. The user can get data into the terminal (or another
output) in a different format - csv, json, table, value, yaml (table is default), and specify the column(s) to show. In
additional there are CSV format options, user can quote
or unquote or partly quote output values - all, minimal, none, non-numeric (by default only non-numeric values are
quoted)Example of output for the --help options for the  command:$cosmosidfiles--help
usage:cosmosidfiles[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--noindent][--max-width<integer>][--fit-width][--print-empty][--quote{all,minimal,none,nonnumeric}][--parentPARENT][--order{type,name,id,status,size,created}][--up]Showfilesinagivendirectory.

optionalarguments:-h,--helpshowthishelpmessageandexit--parentPARENT,-pPARENTIDoftheparentdirectory.Default:Root--order{type,name,id,status,reads,created},-o{type,name,id,status,size,created}fieldforordering--uporderdirection

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeated

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumericTo retrieve files (samples) stored in CosmosID simply run thecosmosidcommand with afilessubcommand. For example:#to get contents of your CosmosID root foldercosmosidfiles#to get contents of appropriate folder use its id as argumentcosmosidfiles--parent=<folder_id>#to get ordered list simply use the ordering argument with field name with/without order directioncosmosidfiles--parent=<folder_id>--ordersize--upRetrieve Sample RunsAn each file (sample) stored in CosmosID has one or more Sample Run(s) associated with it.Example of output for the --help options for the  command:$cosmosidruns--help

usage:cosmosidruns[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending]--idID[--order{id,status,created}][--up]ShowListOfRunsforagivenFile.

optionalarguments:-h,--helpshowthishelpmessageandexit--idID,-iIDIDofthesample--order{id,status,created},-o{id,status,created}fieldforordering--uporderdirection

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.For example:
To retrieve sample run(s) associated with a file simply run thecosmosidcommand withrunssubcommand.#to get runs associated with a speciffic file (sample)cosmosidruns--id=<file_id>Upload filesThe CosmosID-HUB CLI supports uploading sample files into CosmosID for analysis.
CosmosID supports the following file formats and extension names:
.fasta, .fna, .fasta.gz, .fastq, .fq, .fastq.gz, bam, bam.gz, sra, sra.gz. (SRA files can be uploaded without extension)CosmosID supports the following types of analysis:MetagenomicsAmplicon - 16S or ITS (only 16S and ITS supported for now)Note: you can get usage help for each command and arguments of CosmosID-HUB CLI by simply runnigcosmosid --helporcosmosid <command> --help# cosmosid upload --helpusage:cosmosidupload[-h][--fileFILE][--parentPARENT]--type{metagenomics,amplicon-16s,amplicon-its}[-wfWORKFLOW][--forward-primerFORWARD_PRIMER][--reverse-primerREVERSE_PRIMER][--amplicon-preset{v1_v3,v3_v4,v4}][--host-name{human:2.0.0,human:1.0.0,dog:2.0.0,domestic_cat:2.0.0,cow:1.0.0,chicken:2.0.0,mouse:2.0.0,monkey:2.0.0,cattle:2.0.0,pig:2.0.0}][--dirDIR]Uploadfilestocosmosid.

optionalarguments:-h,--helpshowthishelpmessageandexit--fileFILE,-fFILEfile(s)forupload.Supportedfiletypes:fasta,fna,fasta.gz,fastq,fq,fastq.gz,bam,srae.g.cosmosidupload-f/path/file1.fasta-f/path/file2.fn--parentPARENT,-pPARENTcosmosidparentfolderIDforupload--type{metagenomics,amplicon-16s,amplicon-its},-t{metagenomics,amplicon-16s,amplicon-its}Typeofanalysisforafile-wfWORKFLOW,--workflowWORKFLOWTospecifymultipleworkflows,definethemcomaseparatedwithoutanyadditionalsymbols.Forexample:-wfamr_vir,taxa--forward-primerFORWARD_PRIMEROnlyfor'ampliseq'workflow--reverse-primerREVERSE_PRIMEROnlyfor'ampliseq'workflow--amplicon-preset{v1_v3,v3_v4,v4}Onlyfor'ampliseq'workflowv1_v3:-forward_primer:AGAGTTTGATCCTGGCTCAG-reverse_primer:ATTACCGCGGCTGCTGGv3_v4:-forward_primer:CCTACGGGRSGCAGCA-reverse_primer:GACTACHVGGGTATCTAATCCv4:-forward_primer:GTGYCAGCMGCCGCGGTAA-reverse_primer:GGACTACHVGGGTWTCTAAT--host-name{human:2.0.0,human:1.0.0,dog:2.0.0,domestic_cat:2.0.0,cow:1.0.0,chicken:2.0.0,mouse:2.0.0,monkey:2.0.0,cattle:2.0.0,pig:2.0.0}Nameforhostremoval.*Availableonlyfortype`metagenomics`human:2.0.0-Human2.0.0(GCF_009914755.1_T2T-CHM13v2.0)human:1.0.0-Human1.0.0(GRCh38_p6)dog:2.0.0-Dog(GCF_014441545.1_ROS_Cfam_1.0)domestic_cat:2.0.0-DomesticCat(GCF_018350175.1_F.catus_Fca126_mat1.0)cow:1.0.0-Cow(GCF_002263795l_1_ARS-UCD1_2)chicken:2.0.0-Chicken(GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b)mouse:2.0.0-Mouse(GCF_000001635.27_GRCm39)monkey:2.0.0-Monkey(GCF_003339765.1_Mmul_10)cattle:2.0.0-Cattle(GCF002263795.2-ARS-UCD1.3)pig:2.0.0-Pig(GCF_000003025.6_Sscrofa11.1)--dirDIR,-dDIRdirectorywithfilesforuploade.g.cosmosidupload-d/path/my_dirTo upload sample file to CosmosID runcosmosidcommand withuploadsubcommand. By default samples will be uploaded
into root folder. To upload sample into specificexistingfolder you must use id of the folder as parameter.
The CosmosID-HUB CLI supports uploading multiple Single-Read and Paired-End samples. For Paired-End samples, the CLI
automatically parse and merge samples in pairs if the samples follow the naming conventions like: xxx_R1.fastq and
xxx_R2.fastq OR xxx_R1_001.fastq and xxx_R2_001.fastq. Note: Paired-End samples require "fastq" formatTo upload all samples from folder runcosmosid uploadcommand with path to folder specified by --dir/-d parameterNote:This command respects Paired-End samples grouping with the same rules as for regular uploadNote:The default workflow istaxa, that is not allowed for amplicon samples, and should be overriden by--workflowargument.Running example:cosmosid upload --type metagenomics -f /pathtofile/test1_R1.fastq-f /pathtofile/test1_R2.fastq -f
/pathtofile/test2.fasta#to upload one sample file for Metagenomics analysiscosmosidupload--file<pathtofile>--typemetagenomics#to upload sample file into specific folder for Amplicon 16s analysiscosmosidupload--file<pathtofile-1>--parent<folderid>--typeamplicon-16s#to upload all files from foldercosmosidupload-d/home/user/samples/--typemetagenomics#to upload with host-removalcosmosidupload--file<pathtofile>--typemetagenomics--host-name<hostname>#to upload ampliseq-batchcosmosidupload--file<pathtofile>--typeamplicon-16s--workflowampliseq--amplicon-preset<preset>
cosmosidupload--file<pathtofile>--typeamplicon-16s--workflowampliseq--forward-primer<forwardprimer>--reverse-primer<reverseprimer>Note: uploading of a big file takes time, please be patient
Available host names: human:2.0.0, human:1.0.0, dog:2.0.0, domestic_cat:2.0.0, cow:1.0.0, chicken:2.0.0, mouse:2.0.0, monkey:2.0.0, cattle:2.0.0, pig:2.0.0Once file has been uploaded to CosmosID the analyzing process will automatically begin.
You can check the status of metagenomics analysis on the pageCosmosID Samples.
Amplicon analysis results available only from CosmosID-HUB CLI for now.Retrieving Analysis ResultsAnalysis results can be retrieved from CosmosID by useing run id or file id. The latest run analysis results will be
retrieved when file id used.
To retrieve analysis results for a specified run in CosmosID simply runcosmosidcommand withanalysissubcommand.$cosmosidanalysis--help
usage:cosmosidanalysis[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending][--idID][--run_idRUN_ID][--order{database,id,strains,strains_filtered,status}][--up]ShowAnalysisforagivenfile.

optionalarguments:-h,--helpshowthishelpmessageandexit--idID,-iIDIDofafile--run_idRUN_ID,-rRUN_IDIDofasamplerun--order{database,id,strains,strains_filtered,status},-o{database,id,strains,strains_filtered,status}fieldforordering--uporderdirection

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.For example:#to get list of analysis for the latest run of filecosmosidanalysis--id=<fileID>#to get list of analysis for a given run idcosmosidanalysis--run_id=<runID>#to get ordered list of analysis for a given file id simply use ordering argument with field name with/without order directioncosmosidanalysis--id=<fileID>--ordercreated--upNote: There is no analysis results for Amplicon 16S and Amplicon ITS sample. Use report generation instead of getting
list of analysis for Amplicon 16S and Amplicon ITS.Generate Analysis Report ArchiveThe CosmosID-HUB CLI supports retrieving the archive of analysis reports from CosmosID for a givenFile IDwith a
givenRun IDand saving the archive to a given file.To retrieve an analysis report archive with TSV files run thecosmosidcommand withreportssubcommand.$cosmosidreports--help
usage:cosmosidreports[-h]--idID[--outputOUTPUT|--dirDIR]GetanalysisreportsTSV

optionalarguments:-h,--helpshowthishelpmessageandexit--idID,-iIDIDofcosmosidsample.--outputOUTPUT,-oOUTPUToutputfilename.Musthave.zipextension.Default:isequivalenttocosmosidfilename.--dirDIR,-dDIROutputdirectoryforafile.Default:iscurrentdirectory.For example:# to create analysis report archive for the latest run of sample and save it in# a current directory with a name equivalent to file name in CosmosIDcosmosidreports--id=<fileID># to create analysis report archive for the given run of sample and save it in# a current directory with a name equivalent to file name in CosmosIDcosmosidreports--id=<fileID>--run_id=<runID># to create analysis report archive for the given run of sample and save it# in a given directorycosmosidreports--id=<fileID>--run_id=<runID>--dir~/cosmosid/reports# to create analysis report archive for the given run of sample and save it# into a given local filecosmosidreports--id=<fileID>--output/tmp/analysis_report.zipRetrieving Artifacts ResultsArtifacts results can be retrieved from CosmosID by using run id.
To retrieve artifacts results for a specified run in CosmosID simply runcosmosidcommand withartifactssubcommand.$cosmosidartifacts--help
usage:cosmosidartifacts[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending]--run_idRUN_ID[--type{fastqc-zip}][--url][--outputOUTPUT][--dirDIR]ShowArtifactsforagivenfile.

optionalarguments:-h,--helpshowthishelpmessageandexit--run_idRUN_ID,-rRUN_IDIDofasamplerun--type{fastqc-zip},-t{fastqc-zip}Artifacttypetodownload--urlshowdownloadurl--outputOUTPUT,-oOUTPUToutputfilename.Musthave.zipextension.Default:isequivalenttocosmosidfilename.--dirDIR,-dDIROutputdirectoryforafile.Default:iscurrentdirectory.

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.For example:#to get list of artifacts for a given run idcosmosidartifacts--run_id=<runID>##to create artifacts archive for the given run id of sample and store it to given pathcosmosidartifacts--run_id=<runID>--type=fastqc-zip--dir/home/user##to create artifacts archive for the given run id of sample and store it with given name in current dircosmosidartifacts--run_id=<runID>--type=fastqc-zip--outputartifacts_report.zip##to create artifacts archive for the given run id of sample and store it with given name and given dircosmosidartifacts--run_id=<runID>--type=fastqc-zip--dir/home/user--outputartifacts_report.zip#to get url to download the archivecosmosidartifacts--run_id=<runID>--type=fastqc-zip--urlDownload Original SamplesOriginal samples can be downloaded from CosmosID by using samples_ids.
To download samples for a specified samples_id in CosmosID simply runcosmosidscommand withdownloadsubcommand.Note: We recommend installing pycurl for the best experience with a sample download,
see:http://pycurl.io/docs/latest/index.html#installation$cosmosiddownload--help
usage:cosmosiddownload[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending][--samples_idsSAMPLES_IDS][--input-fileINPUT_FILE][--dirDIR][--no-display][--concurrent-downloadsCONCURRENT_DOWNLOADS]DownloadSamplesforagivensamplesids.

optionalarguments:-h,--helpshowthishelpmessageandexit--samples_idsSAMPLES_IDS,-sSAMPLES_IDSCommaseparatedlistofsamplesuuids--input-fileINPUT_FILEPathtofilewithsamples'ids--dirDIR,-dDIROutputdirectoryforafile.Default:iscurrentdirectory.--no-displayDisabledisplayingloadingprocess--concurrent-downloadsCONCURRENT_DOWNLOADSLimitconcurrentfilesdownloads

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.For example:#to download the original samples and save them in the current dircosmosiddownload--samples_ids=<sample_id>#to download the originals samples and save them in the current dircosmosiddownload--samples_ids=<sample_id>,<sample_id>#separated by comma ","#to download the originals samples and store them in the given pathcosmosiddownload--samples_ids=<sample_id>,<sample_id>--dir=<path_to_directory>#to download the originals samples without displaying download progresscosmosiddownload--samples_ids=<samples_id>,<sample_id>--no-display#to download the original samples with specified quantity of concurrent files downloadscosmosiddownload--samples_ids=<sample_id>,<sample_id>--concurrent-downloads=<quantity>#to download the original samples using file with their idscosmosiddownload--input-file=<path-to-file>Note: You can specify chunk size by CHUNK_SIZE environment variableComparative analysisIt's possible to view list of comparative analyses and download them.List commands#print list of comparatives generated using metadata & cohorts menucosmosidcomparatives--help
cosmosidcomparatives--help
usage:cosmosidcomparatives[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending]Listofcomparatives

optionalarguments:-h,--helpshowthishelpmessageandexitoutputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.Print list of comparatives generated using the comparative analysis menu:$cosmosidcomparativeanalyses--help
usage:cosmosidcomparativeanalyses[-h][-f{csv,json,table,value,yaml}][-cCOLUMN][--quote{all,minimal,none,nonnumeric}][--noindent][--max-width<integer>][--fit-width][--print-empty][--sort-columnSORT_COLUMN][--sort-ascending|--sort-descending][--comparative-idCOMPARATIVE_ID]Listofallcomparativeanalysesoutsidecomparatives(iftherearenoanycomparativeids)optionalarguments:-h,--helpshowthishelpmessageandexit--comparative-idCOMPARATIVE_IDComparatives'ids

outputformatters:outputformatteroptions-f{csv,json,table,value,yaml},--format{csv,json,table,value,yaml}theoutputformat,defaultstotable-cCOLUMN,--columnCOLUMNspecifythecolumn(s)toinclude,canberepeatedtoshowmultiplecolumns--sort-columnSORT_COLUMNspecifythecolumn(s)tosortthedata(columnsspecifiedfirsthaveapriority,non-existingcolumnsareignored),canberepeated--sort-ascendingsortthecolumn(s)inascendingorder--sort-descendingsortthecolumn(s)indescendingorder

CSVFormatter:--quote{all,minimal,none,nonnumeric}whentoincludequotes,defaultstononnumeric

jsonformatter:--noindentwhethertodisableindentingtheJSON

tableformatter:--max-width<integer>Maximumdisplaywidth,<1todisable.YoucanalsousetheCLIFF_MAX_TERM_WIDTHenvironmentvariable,buttheparametertakesprecedence.--fit-widthFitthetabletothedisplaywidth.Impliedif--max-widthgreaterthan0.SettheenvironmentvariableCLIFF_FIT_WIDTH=1toalwaysenable--print-emptyPrintemptytableifthereisnodatatoshow.Example: print list of child comparatives generated under a parent comparative using metadata & cohorts menu$cosmosidcomparativeanalyses--comparative-id=<comparative_id>Export commandsExport comparative analyses without log scale$cosmosidcomparativeanalysesexport--help
usage:cosmosidcomparativeanalysesexport[-h]--idID[--tax-level{kingdom,order,phylum,class,family,genus,species,strain}][--log-scale][--concurrent-downloadsCONCURRENT_DOWNLOADS][--dirDIR]Downloadresultsofcomparativeanalyses

optionalarguments:-h,--helpshowthishelpmessageandexit--idIDIDsofcomparativeanalyses--tax-level{kingdom,order,phylum,class,family,genus,species,strain}Taxonomy--log-scaleIncludesresultswithlogscale--concurrent-downloadsCONCURRENT_DOWNLOADSLimitconcurrentfilesdownloads--dirDIR,-dDIROutputdirectoryforafile.Default:iscurrentdirectory.Example export comparative analyses with specified taxonomy level ('species' by default):$cosmosidcomparativeanalysesexport--id=<analysis_id>--tax-level=class--tax-level=genus