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<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.1.0">
	<description>
	</description>
	
	<requirements>
        <requirement type="binary">genomeCoverageBed</requirement>
    </requirements>
    
	<command>genomeCoverageBed
        #if $input.ext == "bam"
            -ibam '$input'
        #else
            -i '$input'
            -g ${chromInfo}
        #end if
		#if str($max):
          -max      $max
        #end if
		&gt; '$output'
	</command>

	<inputs>
		<param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
		<param name="max" type="text" optional="true" label="Max depth" help="Combine all positions with a depth >= max into a single bin in the histogram."/>
	</inputs>

	<outputs>
		<data format="tabular" name="output"  metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
	</outputs>

<help>
**What it does**

This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.


------

.. class:: warningmark

This tool requires that `bedtools`__ has been installed on your system.

.. class:: infomark

The output file 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




------

This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__

    .. __: http://code.google.com/p/bedtools/
    .. __: http://code.google.com/p/bedtools/
    .. __: http://cphg.virginia.edu/quinlan/
    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short



</help>
</tool>