view macs2_bdgbroadcall.xml @ 4:9c88d83c2690 draft

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<tool id="macs2_bdgbroadcall" name="Call broad peaks" version="2.0.10.0">
    <description>from bedGraph</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>

        macs2 bdgbroadcall
            --ifile $infile
            --cutoff-peak $cutoffpeak
            --cutoff-link $cutofflink
            --min-length $minlen
            --lvl1-max-gap $LVL1MAXGAP
            --lvl2-max-gap $LVL2MAXGAP
            --ofile $ofile

    </command>
    <inputs>

        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" help="depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2.0 (--cutoff-peak)"/>
        <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="better to set it as d value" />
        <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" help="better to set it as tag size" />
        <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" help="better to set it as 4 times of d value" />

    </inputs>

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

Call broad peaks from bedGraph output.
bdgbroadcall from macs2

------

**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>