<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="2.0.10.0">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 refinepeak
            -b "${ bed_infile }"
            -i "${ infile }"
            --format '${ infile.extension.upper() }'
            --cutoff "${ cutoff }"
            --window-size "${ winsize }"
            --ofile "${ outfile }"
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
        <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
        <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />
    </inputs>

    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="ChIP_200K.bed" ftype="bed"/>
            <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/>
            <param name="cutoff" value="5.0"/>
            <param name="winsize" value="200"/>
            <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/>
        </test>
    </tests>
    <help>
**What it does**

(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.

@citation@
    </help>
</tool>
