<macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <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>
            <yield />
        </citations>
    </xml>
</macros>
