<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set inputBs = "' '".join([str($file) for $file in $inputB])

        bedtools coverage
        $d
        $hist
        $split
        $strandedness
        -a '$inputA'
        -b '$inputBs'
        | sort -k1,1 -k2,2n
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
        <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
        <expand macro="split" />
        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
            help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
        <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
            label="Report the depth at each position in each A 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 A as well as a summary histogram for all features in A"
            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.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**

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

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

.. class:: infomark

The lines in the output will be comprised of each interval in A, followed by:

1. The number of features in B that overlapped (by at least one base pair) the A interval.
2. The number of bases in A that had non-zero coverage from features in B.
3. The length of the entry in A.
4. The fraction of bases in A that had non-zero coverage from features in B.

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