<macros>
    <token name="@TOOL_VERSION@">0.8</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@profile@">22.05</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">rbpbench</requirement>
            <requirement type="package" version="5.5.4">meme</requirement>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">rbpbench</xref>
        </xrefs>
    </xml>
    <!--xml name="citations">
        <citations>
            <citation type="doi"></citation>
        </citations>
    </xml-->
    <token name="@PREPARE_REF@"><![CDATA[
        ln -s -f
        #if str($action_type.reference_genome.reference_genome_selector) == "history"
            '$action_type.reference_genome.history_genome'
        #else
            '$action_type.reference_genome.builtin_genome.fields.path'
        #end if
        reference.fa &&
    ]]></token>
    <token name="@COMMON_PARAMS@"><![CDATA[
        --ext $action_type.search_options.search_ext
        --fimo-pval $action_type.search_options.search_fimo_pval
        --bed-score-col $action_type.search_options.search_bed_score_col
        $action_type.search_options.search_unstranded
        $action_type.search_options.search_unstranded_ct
        #if $action_type.search_options.fimo_nt_freqs_file:
            --fimo-nt-freqs '$action_type.search_options.fimo_nt_freqs_file'
        #end if
    ]]></token>
</macros>