<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
    <description>Call broad peaks from bedGraph output</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgbroadcall
            --ifile '${ infile }'
            --cutoff-peak '${ cutoffpeak }'
            --cutoff-link '${ cutofflink }'
            --min-length '${ minlen }'
            --lvl1-max-gap '${ LVL1MAXGAP }'
            --lvl2-max-gap '${ LVL2MAXGAP }'
            --ofile "macs2_bdgbroadcall.bdg"
        &&
        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
            help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/>
        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
            help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. Default=1 (--cutoff-link)"/>
        <param name="minlen" type="integer" label="Minimum length of peak" value="200"
            help="It is recommended to set it as d value. Default=200 (--min-length)" />
        <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
            help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
        <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
            help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
    </inputs>
    <outputs>
        <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
            <param name="cutoffpeak" value="2.0"/>
            <param name="cutofflink" value="1.0"/>
            <param name="minlen" value="200"/>
            <param name="LVL1MAXGAP" value="30"/>
            <param name="LVL2MAXGAP" value="800"/>
            <output name="outfile" file="bdgbroadcall_output.bdg"/>
        </test>
    </tests>
    <help>
**What it does**

This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.

.. _MACS2: https://github.com/taoliu/MACS


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