<tool id="collection_element_identifiers" name="Extract element identifiers" version="0.0.2">
    <description>of a list collection</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
mv '$cf' '$output'
    ]]>
    </command>
    <configfiles>
        <configfile name="cf">#for $el in $input_collection:
${el.element_identifier}
#end for</configfile>
    </configfiles>
    <inputs>
        <param name="input_collection" type="data_collection" collection_type="list,list:paired" label="Dataset collection"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_collection">
                <collection type="list">
                    <element name="e1" value="simple_line.txt" />
                    <element name="e2" value="simple_line.txt" />
                    <element name="e3" value="simple_line.txt" />
                </collection>
            </param>
            <output name="output" file="output_1.txt" />
        </test>
        <test>
            <param name="input_collection">    
                <collection type="list:paired">
                    <element name="pair1">
                        <collection type="paired">
                            <element name="forward" value="simple_line.txt" />
                            <element name="reverse" value="simple_line.txt" />
                        </collection>
                    </element>
                    <element name="pair2">
                        <collection type="paired">
                            <element name="forward" value="simple_line.txt" />
                            <element name="reverse" value="simple_line.txt" />
                        </collection>
                    </element>
                </collection>
            </param>
            <output name="output" file="output_2.txt"/>
        </test>
    </tests>
    <help><![CDATA[
This tool takes a list-type collection and produces a text dataset as output, containing the element identifiers of all datasets contained in the collection.
    ]]></help>
    <citations>
    </citations>
</tool>