annotate organism_add_organism.xml @ 15:680a1fe3c266 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"

<?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>