<?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>