Mercurial > repos > gga > tripal_organism_get_organisms
diff organism_get_organisms.xml @ 0:791692de64d6 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
| author | gga |
|---|---|
| date | Mon, 11 Sep 2017 05:53:54 -0400 |
| parents | |
| children | 0285d79f211e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/organism_get_organisms.xml Mon Sep 11 05:53:54 2017 -0400 @@ -0,0 +1,64 @@ +<?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>