view macs2_predict.xml @ 1:d202e3d663bb draft

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<tool id="macs2_predict" name="Predict" version="2.0.10.0">
    <description>d or fragment size from alignment results</description>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
    </expand>
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 predict
            -i #echo ','.join($infiles)#
            --tsize $tsize
            @effective_genome_size@
            --bw $band_width
            --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
            &gt; $outfile;

        Rscript predicted_model.R &gt; $outfile_image
    </command>
        <expand macro="stdio" />
    <inputs>
        <repeat name="infiles" title="ChIP-seq alignment files" min="1" 
            help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">

            <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
        </repeat>

        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />

        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
            help="This value is only used while building the shifting model. (--bw)" />

        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>

    </inputs>

    <outputs>
        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </tests>
    <help>
**What it does**

bdgdiff from macs2


Note that pair-end data is not supposed to work with this command.


------

**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>