<macros>
    <token name="@DEEPTOOLS_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "bamPEFragmentSize"
                #set $pattern = "Frag."
                @LN_2_FILES@
            #elif str($repeat2.type) == "estimateReadFiltering"
                #set $pattern = "Internally-determined Duplicate"
                @LN_2_FILES@
            #elif str($repeat2.type) == "plotCoverageStdout"
                #set $pattern = "sample"
                @LN_2_FILES@
            #elif str($repeat2.type) == "plotCoverageOutRawCounts"
                #set $pattern = "#plotCoverage --outRawCounts"
                @LN_2_FILES@
            #elif str($repeat2.type) == "plotEnrichment"
                #set $pattern = "featureReadCount"
                @LN_2_FILES@
            #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
                #set $pattern = "#plotFingerprint --outRawCounts"
                @LN_2_FILES@
            #end if
        #end for
    ]]></token>
    <xml name="deeptools_form">
        <repeat name="output" title="deepTools output" min="1">
            <param name="type" type="select" label="deepTool used to generate the output?">
                <option value="bamPEFragmentSize">bamPEFragmentSize</option>
                <option value="estimateReadFiltering">estimateReadFiltering</option>
                <option value="plotCoverageStdout">plotCoverageStdout</option>
                <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option>
                <option value="plotEnrichment">plotEnrichment</option>
                <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option>
                <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
            </param>
            <param name="input" type="data" format="txt" label="Bismark output" multiple="true"/>
        </repeat>
    </xml>
</macros>