<macros>
    <token name="@PICARD_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "alignment_metrics"
                #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "basedistributionbycycle"
                #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "gcbias"
                #set $pattern = "picard.analysis.GcBias"
                @LN_2_FILES@
            #elif str($repeat2.type) == "hsmetrics"
                #set $pattern = "picard.analysis.directed.HsMetrics"
                @   @
            #elif str($repeat2.type) == "insertsize"
                #set $pattern = "picard.analysis.InsertSizeMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "markdups"
                #set $pattern = "MarkDuplicates"
                @LN_2_FILES@
            #elif str($repeat2.type) == "oxogmetrics"
                #set $pattern = "picard.analysis.CollectOxoGMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "pcr_metrics"
                #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "rnaseqmetrics"
                #set $pattern = "Collect"
                @LN_2_FILES@
            #elif str($repeat2.type) == "rrbs_metrics"
                #set $pattern = "picard.analysis.RrbsSummaryMetrics"
                @LN_2_FILES@
            #elif str($repeat2.type) == "wgs_metrics"
                #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
                @LN_2_FILES@
            #end if
        #end for
    ]]></token>
    <xml name="picard_form">
        <repeat name="output" title="Picard output" min="1">
            <param name="type" type="select" label="Type of Picard output?">
                <option value="alignment_metrics">Alignment metrics</option>
                <option value="basedistributionbycycle">Base distribution by cycle</option>
                <option value="gcbias">GC bias</option>
                <option value="hsmetrics">HS Metrics</option>
                <option value="insertsize">Insert size</option>
                <option value="markdups">Markdups</option>
                <option value="oxogmetrics">Oxog metrics</option>
                <option value="pcr_metrics">PCR metrics</option>
                <option value="rnaseqmetrics">RNA Seq metrics</option>
                <option value="rrbs_metrics">RRBS metrics</option>
                <option value="wgs_metrics">WGS metrics</option>
            </param>
            <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
        </repeat>
    </xml>
    <xml name="picard_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="picard"/>
                    <repeat name="output">
                        <param name="type" value="gcbias"/>
                        <param name="input" value="picard_collectGcBias.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="insertsize"/>
                        <param name="input" value="picard_CollectInsertSizeMetrics.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="markdups"/>
                        <param name="input" value="picard_MarkDuplicates.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="basedistributionbycycle"/>
                        <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="rnaseqmetrics"/>
                        <param name="input" value="picard_CollectRnaSeqMetrics.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="alignment_metrics"/>
                        <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="picard_CollectRnaSeqMetrics_bam"/>
                    <has_text text="picard_alignment_readlength"/>
                    <has_text text="picard-rna-assignment"/>
                    <has_text text="picard-markduplicates"/>
                    <has_text text="picard-insertsize"/>
                    <has_text text="picard-gcbias"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="picard_CollectRnaSeqMetrics_bam"/>
                    <has_text text="InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_median"/>
                    <has_text text="picard_CollectRnaSeqMetrics_bam"/>
                    <has_text text="RnaSeqMetrics_mqc_generalstats_picard_rnaseqmetrics_PCT_MRNA_BASES"/>
                    <has_text text="NA"/>
                    <has_n_lines n="4"/>
                    <has_n_columns n="6"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="3"/>
        </test>
    </xml>
</macros>