<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools bedpetobam
        $ubam
        -mapq $mapq
        -i '$input'
        -g $genome
        &gt; '$output'
    </command>
    <inputs>
        <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
        <expand macro="genome" />
        <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
        <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
    </inputs>
    <outputs>
        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
    </outputs>
    <help>

**What it does**

Converts feature records to BAM format.

.. class:: warningmark

BED files must be at least BED4 to create BAM (needs name field).

@REFERENCES@
    </help>
</tool>