<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@WRAPPER_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools bedpetobam
            -mapq $mapq
            -i '$input'
            -g @GENOME_FILE@
            > '$output'
]]>
    </command>
    <inputs>
        <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="input_conditional_genome_file" />
        <param name="mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
            help="(-mapq)" />
    </inputs>
    <outputs>
        <data format="bam" name="output" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len"/>
            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>
    <expand macro="citations" />
</tool>