comparison macs2_bdgbroadcall.xml @ 9:acbd3fb47f90 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2

8:e8a060164e11

    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
         <![CDATA[
        macs2 bdgbroadcall
            --ifile '${ infile }'
            --cutoff-peak '${ cutoffpeak }'
            --cutoff-link '${ cutofflink }'
            --min-length '${ minlen }'
            --lvl1-max-gap '${ LVL1MAXGAP }'
            --lvl2-max-gap '${ LVL2MAXGAP }'
            --ofile "macs2_bdgbroadcall.bdg"
        &&
        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
        ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
            help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/>
        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"

9:acbd3fb47f90

    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgbroadcall
            --ifile '${ infile }'
            --cutoff-peak '${ cutoffpeak }'
            --cutoff-link '${ cutofflink }'
            --min-length '${ minlen }'
            --lvl1-max-gap '${ LVL1MAXGAP }'
            --lvl2-max-gap '${ LVL2MAXGAP }'
            --ofile "macs2_bdgbroadcall.bdg"
        &&
        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
            help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/>
        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"