Mercurial > repos > gga > chado_organism_get_organisms
diff organism_get_organisms.xml @ 0:1ce80eabf7eb draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
| author | gga |
|---|---|
| date | Thu, 21 Jun 2018 08:45:28 -0400 |
| parents | |
| children | 05e1fd17832b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/organism_get_organisms.xml Thu Jun 21 08:45:28 2018 -0400 @@ -0,0 +1,54 @@ +<?xml version="1.0"?> +<tool id="organism_get_organisms" name="Chado organism get" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +@AUTH@ + +chakin 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> + <!-- arguments --> + + <!-- options --> + <param name="organism_id" label="Organism Id" argument="organism_id" type="integer" help="organism_id filter" optional="True" /> + <param name="genus" label="Genus" argument="genus" type="text" help="genus filter" optional="True" /> + <param name="species" label="Species" argument="species" type="text" help="species filter" optional="True" /> + <param name="common" label="Common" argument="common" type="text" help="common filter" optional="True" /> + <param name="abbr" label="Abbr" argument="abbr" type="text" help="abbr filter" optional="True" /> + <param name="comment" label="Comment" argument="comment" type="text" help="comment filter" optional="True" /> + + </inputs> + <outputs> + <data format="json" name="results"/> + </outputs> + <help> +Get all or some organisms + +@HELP@ + </help> +</tool>