<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4">
<description></description>

<requirements>
    <requirement type="binary">bamToBed</requirement>
</requirements>

<command>
    bamToBed $option $ed_score -i '$input' &gt; '$output' 
    #if str($tag):
      -tag      $tag
    #end if
</command>

<inputs>
    <param format="bam" name="input" type="data" label="Input BAM file"/>
    <param name="option" type="select" label="Output formatting options">
        <option value="">Create a 6-column BED file.</option>
        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
    </param>
    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/>
    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
</inputs>

<outputs>
    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
</outputs>

<help>

**What it does**

This tool converts a BAM file to a BED file. The end coordinate is computed
by inspecting the CIGAR string. The QNAME for the alignment is used as the 
BED name field and, by default, the MAPQ is used as the BED score.

------


This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.

.. __: http://code.google.com/p/bedtools/
.. __: http://cphg.virginia.edu/quinlan/

</help>
</tool>