<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@">
    <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
@OVERLAP@
$reciprocal
$split
-q $q
$duplicate
$failed
$proper
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
        <!-- Additional files, if the user needs more -->
        <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" />

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