<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
    <description>compute the coverage over an entire genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools genomecov
        #if $input.ext == "bam"
            -ibam '$input'
        #else
            -i '$input'
            -g $genome
        #end if

        $split
        $strand

        #if str($report.report_select) == "bg":
            #if $report.zero_regions:
                $report.zero_regions
            #else:
                -bg
            #end if

            #if str($report.scale):
              -scale $report.scale
            #end if
        #else:
            #if str($report.max):
              -max $report.max
            #end if
        #end if
        $d
        $dz
        $five
        $three

        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
              <validator type="unspecified_build" />
        </param>
        <conditional name="report">
            <param name="report_select" type="select" label="Output type">
                <option value="bg" selected="true">BedGraph coverage file</option>
                <option value="hist">Data suiteable for Histogram</option>
            </param>
            <when value="bg">
                <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
                <param name="scale" type="float" value="1.0"
                    label="Scale the coverage by a constant factor"
                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/>
            </when>
            <when value="hist">
                <param name="max" type="integer" label="Specify max depth" value="0"
                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
            </when>
        </conditional>
        <expand macro="genome" />
        <expand macro="split" />
        <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
            <option value="">both strands combined</option>
            <option value="-strand +">positive strand only</option>
            <option value="-strand -">negative strand only</option>
        </param>

        <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue=""
            label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
        <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
            label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
        <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue=""
            label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
        <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
            label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
    </inputs>
    <outputs>
        <data format="bedgraph" name="output">
            <change_format>
                <when input="report.report_select" value="hist" format="tabular" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
            <param name="genome" value="genomeCoverageBed1.len" />
            <param name="report_select" value="hist" />
            <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.

.. image:: $PATH_TO_IMAGES/genomecov-glyph.png

.. class:: warningmark

The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).

-----

**Example 1**

Input (BED format)-
Overlapping, un-sorted intervals::

    chr1    140 176
    chr1    100 130
    chr1    120 147


Output (BedGraph format)-
Sorted, non-overlapping intervals, with coverage value on the 4th column::

    chr1    100 120 1
    chr1    120 130 2
    chr1    130 140 1
    chr1    140 147 2
    chr1    147 176 1

-----

**Example 2 - with ZERO-Regions selected (assuming hg19)**

Input (BED format)-
Overlapping, un-sorted intervals::

    chr1    140 176
    chr1    100 130
    chr1    120 147


BedGraph output will contain five columns:

    * 1. Chromosome name (or 'genome' for whole-genome coverage)
    * 2. Coverage depth
    * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
    * 4. The size of chromosome (or entire genome) in base pairs
    * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.

**Example Output**:
    
    chr2L       0           1379895     23011544    0.0599653
    chr2L       1           837250      23011544    0.0363839
    chr2L       2           904442      23011544    0.0393038
    chr2L       3           913723      23011544    0.0397072
    chr2L       4           952166      23011544    0.0413778
    chr2L       5           967763      23011544    0.0420555
    chr2L       6           986331      23011544    0.0428624
    chr2L       7           998244      23011544    0.0433801
    chr2L       8           995791      23011544    0.0432735
    chr2L       9           996398      23011544    0.0432999


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