<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
    <requirements>
        <requirement type="package" version="2.27.1">bedtools</requirement>
    </requirements>
    <expand macro="stdio" />
    <command><![CDATA[
bedtools bedpetobam
-mapq $mapq
-i '$input'
-g @GENOME_FILE@
> '$output'
    ]]></command>
    <inputs>
        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="input_conditional_genome_file" />
        <param argument="-mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
    </inputs>
    <outputs>
        <data name="output" format="unsorted.bam" 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="unsorted.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>