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<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
    <description>of features in file A across the features in file B (coverageBed)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        coverageBed
        #if $inputA.ext == "bam"
            -abam '$inputA'
        #else
            -a '$inputA'
        #end if
        -b '$inputB'
        $split
        $strand
        | sort -k1,1 -k2,2n
        &gt; '$output'
    </command>
    <inputs>
        <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)">
            <validator type="unspecified_build" />
        </param>
        <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)">
            <validator type="unspecified_build" />
        </param>
        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage"
            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data" />
        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
            help="That is, only features in A are only counted towards coverage in B if they are the same strand."/>
    </inputs>

    <outputs>
        <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/>
    </outputs>
    <help>

**What it does**

coverageBed_ computes both the depth and breadth of coverage of features in file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. One advantage that coverageBed offers is that it not only counts the number of features that overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features.
Thus, coverageBed also computes the breadth of coverage for each interval in B.

.. coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html

.. class:: infomark

The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.

@REFERENCES@

    </help>
</tool>