comparison macs2_bdgdiff.xml @ 0:9c157b556c33 draft

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0:9c157b556c33

<tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0">
    <description>based on paired four bedgraph files</description>
    <requirements>
        <requirement type="python-module">macs2</requirement>
        <requirement type="python-module">numpy</requirement>
        <requirement type="package" version="2.0.10.2">macs2</requirement>
        <requirement type="package" version="1.7.1">numpy</requirement>
    </requirements>
    <command>

        macs2 bdgdiff
            --t1 $infile_pileup_cond1
            --t2 $infile_pileup_cond2
            --c1 $infile_control_cond1
            --c2 $infile_control_cond2
            --cutoff $cutoff
            --min-len $minlen
            --depth1 $depth1
            --depth2 $depth2

            # Why does #if '--ofile-cond1' in $outputs not work?
            #if '--ofile-cond1' in str($outputs).split(','):
                --ofile-cond1 $output_cond1
            #end if

            #if '--ofile-cond2' in str($outputs).split(','):
                --ofile-cond2 $output_cond2
            #end if

            #if '--ofile-both-conditions' in str($outputs).split(','):
                --ofile-both-conditions $output_both
            #end if

    </command>
    <inputs>
        <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
        <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />

        <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" />
        <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" />

        <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="DEFAULT: 1.0 (likelihood ratio=10) (--cutoff)"/>
        <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/>
        <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default: 1 (--depth1)" />
        <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default: 1 (--depth2)" />

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
            <option value="--ofile-cond1">Unique regions in condition 1</option>
            <option value="--ofile-cond2">Unique regions in condition 2</option>
            <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
            <validator type="no_options" message="Please select at least one output file." />
        </param>

    </inputs>

    <outputs>
        <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (cond 1)">
            <filter>'--ofile-cond1' in outputs</filter>
        </data>
        <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (cond 2)">
            <filter>'--ofile-cond2' in outputs</filter>
        </data>
        <data name="output_both" format="bed" label="${tool.name} on ${on_string} (both)">
            <filter>'--ofile-both-conditions' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </tests>
    <help>
**What it does**

bdgdiff 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>