Mercurial > repos > gga > tripal_organism_get_organisms
view organism_get_organisms.xml @ 3:13ce6841218c draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1
author | gga |
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date | Mon, 06 Aug 2018 04:45:08 -0400 |
parents | 791692de64d6 |
children | 0285d79f211e |
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<?xml version="1.0"?> <tool id="organism_get_organisms" profile="16.04" name="Get organisms" version="@WRAPPER_VERSION@.0"> <description>from Tripal</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="1.5">jq</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ @AUTH@ tripaille organism get_organisms #if $organism_id: --organism_id "$organism_id" #end if #if $genus: --genus "$genus" #end if #if $species: --species "$species" #end if #if $common: --common "$common" #end if #if $abbr: --abbr "$abbr" #end if #if $comment: --comment "$comment" #end if | jq -S . > $results ]]></command> <inputs> <param name="organism_id" label="Organism Id" argument="organism_id" type="text" optional="true" help="An organism ID" /> <param name="genus" label="Genus" argument="genus" type="text" optional="true" help="The genus of the organism" /> <param name="species" label="Species" argument="species" type="text" optional="true" help="The species of the organism" /> <param name="common" label="Common" argument="common" type="text" optional="true" help="The common name of the organism" /> <param name="abbr" label="Abbr" argument="abbr" type="text" optional="true" help="The abbreviation of the organism" /> <param name="comment" label="Comment" argument="comment" type="text" optional="true" help="A comment / description" /> </inputs> <outputs> <data format="json" name="results" label="Tripal organisms" /> </outputs> <tests> <test expect_failure="true"> <expand macro="test_result" /> </test> </tests> <help><![CDATA[ @HELP_OVERVIEW@ **Get Organisms** With this tool, you can list organisms from the Tripal/Chado database @HELP@ ]]></help> <expand macro="citation"/> </tool>