<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
    <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>
<![CDATA[
        coverageBed
        #if $inputA.ext == "bam"
            -abam '$inputA'
        #else
            -a '$inputA'
        #end if
        -b '$inputB'
        $d
        $hist
        $split
        $strandedness
        | sort -k1,1 -k2,2n
        > '$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)" />
        <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)" />
        <expand macro="split" />
        <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. (-s)"/>
        <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
            label="Report the depth at each position in each B feature"
            help="Positions reported are one based.  Each position and depth follow the complete B feature. (-d)" />
        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
            label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
            help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="inputB" label="Count of overlaps in ${inputA.name} on ${inputB.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
            <param name="genome" value="coverageBedB.bed" ftype="bed" />
            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>
    <expand macro="citations" />
</tool>