comparison macs2_refinepeak.xml @ 36:8c8ae1e19b10 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a

35:2f7d0d0b5bd0

<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 refinepeak
            -b "${ bed_infile }"
            -i "${ infile }"
            --format '${ infile.extension.upper() }'
            --cutoff "${ cutoff }"
            --window-size "${ winsize }"
            --ofile "${ outfile }"
    </command>
    <expand macro="stdio" />
    <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)"/>
        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />

36:8c8ae1e19b10

<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <macros>
        <import>macs2_macros.xml</import>
    </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)"/>
        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />