view macs2_refinepeak.xml @ 4:9c88d83c2690 draft

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<tool id="macs2_refinepeak" name="Refine peak summits" version="2.0.10.0">
    <description></description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>

        macs2 refinepeak
            -b $bed_infile
            -i $infile
            --format '$ifile.extension.upper()'
            --cutoff $cutoff
            --window-size $winsize
            --ofile $ofile

    </command>
    <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="ofile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </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.

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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>