<?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>