<tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0">
    <description>counts coverage from multiple BAMs at specific intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #for $i, $bam in enumerate( $bams ):
            ln -s -f $bam ${i}.bam &&
            ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
        #end for

        bedtools multicov
            -bed $input
            -bams
            #for $i, $bam in enumerate( $bams ):
                ${i}.bam
            #end for
            $strand
            -f $overlap
            $reciprocal
            $split
            -q $q
            $duplicate
            $failed
            $proper
            > $output
]]>
    </command>
    <inputs>
        <param name="input" format="bed" type="data" label="Sorted BED file" />
        <!-- Additional files, if the user needs more -->
        <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />

        <expand macro="strand2" />
        <expand macro="overlap" />
        <expand macro="reciprocal" />
        <expand macro="split" />
        <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
        <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
            label="Include duplicate reads"
            help="Default counts non-duplicates only. (-D)" />
        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
            label="Include failed-QC reads" 
            help="Default counts pass-QC reads only (-F)"/>
        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
            label="Only count proper pairs"
            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
    </inputs>
    <outputs>
        <data name="output" metadata_source="input" format_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="multiCov1.bed" ftype="bed" />
            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
            <param name="q" value="1"/>
            <param name="split" value="False"/>
            <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.


@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>