view organism_add_organism.xml @ 12:6512156f6a17 draft

"planemo upload for repository commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
author gga
date Wed, 21 Aug 2019 05:09:02 -0400
parents e79da6f1f0da
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<?xml version="1.0"?>
<tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@">
	<expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[

chakin organism add_organism

#if $comment:
  --comment '$comment'
#end if

| jq -S . > '$results'

  <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" />

		<data format="json" name="results" label="Chado organism add: ${genus} ${species}"/>
    <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${} '${genus} ${species}' on ${on_string}">
			<filter>psql_target['method'] == "pgtools"</filter>
Add a new organism to the Chado database