<macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">metaQuantome</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="db">
        <param argument="db_tar" type="data" label="Database Archive File"/>
    </xml>
    <xml name="ONTOLOGY_ARGS">
        <conditional name="ontology_args">
            <param name="ontology" type="select" label="Ontology">
                <option value="go">Gene Ontology (GO terms)</option>
                <option value="ec">Enzyme Commission (EC) numbers</option>
                <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
            </param>
            <when value="go">
                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
            </when>
            <when value="ec">
                <!-- do nothing -->
            </when>
            <when value="cog">
                <!-- do nothing -->
            </when>
        </conditional>
    </xml>
    <token name="@COMMON_PARAMS@"><![CDATA[
            --samps '$samps'
            --mode '$mode_args.mode'
            #if $mode_args.mode == 'f'
                --ontology='$mode_args.ontology_args.ontology'
            #end if
            #if $mode_args.mode == 'ft'
                --ontology='$mode_args.ontology_args.ontology'
            #end if
    ]]>
    </token>
    <xml name="SAMPS">
        <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation>
            <yield/>
        </citations>
    </xml>
</macros>