view macs2_bdgpeakcall.xml @ 1:d202e3d663bb draft

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<tool id="macs2_bdgpeakcall" name="Call peaks" version="2.0.10.0">
    <description>from bedGraph output</description>
    <expand macro="requirements" />
    <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 $ofile

    </command>
    <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="ofile" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </tests>
    <help>
**What it does**

Call peaks from bedGraph output.
bdgpeakcall from macs2


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**Citation**

For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Integration of MACS2 with Galaxy performed by Ziru Zhou ( [e-mail] ). Please send your comments/questions to modENCODE DCC at [e-mail].
    </help>
</tool>