<tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
    <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamPEFragmentSize</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
<![CDATA[
        bamPEFragmentSize

        @THREADS@

        --bam '$bamInput'
        --bamIndex ${bamInput.metadata.bam_index}
        #if $histogram:
            --histogram $histogram_outfile
        #end if
        > $outfile

]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>
        <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
            label="Get the distribion of fragment length as histogram"
            help="(--histogram)"/>
    </inputs>
    <outputs>
        <data format="txt" name="outfile" label="${tool.name} on ${on_string}" />
        <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
            <filter>histogram == '--histogram'</filter>
        </data>
    </outputs>
    <help>

**What it does**

Given a BAM file it samples several regions to estimate the paird-end fragment length.

-----

@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>