<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="2.0.10.0">
    <description>Call peaks from bedGraph output</description>
    <expand macro="requirements">
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
    </expand>
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 bdgpeakcall
        --ifile "${ infile }"
        --cutoff "${ cutoff }"
        --min-length "${ minlen }"
        --max-gap "${ maxgap }"
        ${ callsummits }
        ${ notrackline }
        --ofile "macs2_bdgpeakcall.bdg"
        &amp;&amp;
        awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />

        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" 
            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: 5.0 (--cutoff)"/>
        <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/>
        <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/>

        <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" 
            label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region."
            help="(-call-summits)"/>
        <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" 
            label="Include trackline into bedGraph output"
            help="required by USCS (--no-trackline)"/>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" />
            <param name="cutoff" value="5.0"/>
            <param name="minlen" value="200"/>
            <param name="maxgap" value="30"/>
            <output name="outfile" file="bdgpeakcall_on_callpeak_treatment.tabular"/>
        </test>
    </tests>
    <help>
**What it does**

Call peaks from bedGraph output.
bdgpeakcall from macs2


@citation@
    </help>
</tool>
