Mercurial > repos > gga > chado_organism_add_organism
view organism_add_organism.xml @ 20:b37a0f33959d draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 73142be24a0462a3aeb303401e8fcbc72f1cd4f5"
author | gga |
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date | Mon, 14 Mar 2022 14:53:38 +0000 |
parents | 6512156f6a17 |
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<?xml version="1.0"?> <tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ @START_PSQL@ && chakin organism add_organism '$genus' '$species' '$common' '$abbr' #if $comment: --comment '$comment' #end if | jq -S . > '$results' @ZIP_PSQL@ ]]></command> <inputs> <expand macro="psql_target"/> <!-- arguments --> <param name="genus" label="Genus" argument="genus" type="text" help="The genus of the organism" /> <param name="species" label="Species" argument="species" type="text" help="The species of the organism" /> <param name="common" label="Common" argument="common" type="text" help="The common name of the organism" /> <param name="abbr" label="Abbr" argument="abbr" type="text" help="The abbreviation of the organism" /> <!-- options --> <param name="comment" label="Comment" argument="--comment" type="text" help="A comment / description" /> </inputs> <outputs> <data format="json" name="results" label="Chado organism add: ${genus} ${species}"/> <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${genus} ${species}' on ${on_string}"> <filter>psql_target['method'] == "pgtools"</filter> </data> </outputs> <help> Add a new organism to the Chado database @HELP@ </help> </tool>