comparison macs2_refinepeak.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

4:56e104999978

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        macs2 refinepeak
            -b "${ bed_infile }"
            -i "${ infile }"
            --format '${ infile.extension.upper() }'
            --cutoff "${ cutoff }"
            --window-size "${ winsize }"
            --ofile "${ outfile }"
    </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)"/>

    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="ChIP_200K.bed" ftype="bed"/>
            <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/>
            <param name="cutoff" value="5.0"/>
            <param name="winsize" value="200"/>
            <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/>
        </test>
    </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.

@citation@
    </help>
    <expand macro="citations" />
</tool>

5:beb902da6e5f

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        <![CDATA[
        macs2 refinepeak
            -b '${ bed_infile }'
            -i '${ infile }'
            --format '${ infile.extension.upper() }'
            --cutoff '${ cutoff }'
            --window-size '${ winsize }'
            --ofile '${ outfile }'
        ]]>
    </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)"/>

    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="refinepeak_bam_input.bam" ftype="bam"/>
            <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/>
            <param name="cutoff" value="5.0"/>
            <param name="winsize" value="200"/>
            <output name="outfile" file="refinepeak_output.bed"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline.

.. _MACS2: https://github.com/taoliu/MACS
.. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/

@citation@
]]>
    </help>
    <expand macro="citations" />
</tool>