comparison macs2_refinepeak.xml @ 63:25e46cf1ee36 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"

62:1ac88e46ee0f

<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.1">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>

            -i '${ infile }'
            --format '${ infile.extension.upper() }'
            --cutoff '${ cutoff }'
            --window-size '${ winsize }'
            --ofile '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="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="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>

63:25e46cf1ee36

<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>

            -i '${ infile }'
            --format '${ infile.extension.upper() }'
            --cutoff '${ cutoff }'
            --window-size '${ winsize }'
            --ofile '${ outfile }'
            @buffer_size@
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="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)" />
        <expand macro="buffer_size"/>
    </inputs>

    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>