comparison macs2_bdgpeakcall.xml @ 9:acbd3fb47f90 draft

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

8:e8a060164e11

        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        <![CDATA[

        macs2 bdgpeakcall
        --ifile '${ infile }'
        --cutoff '${ cutoff }'
        --min-length '${ minlen }'
        --max-gap '${ maxgap }'
        ${ cutoff_analysis } 
        ${ notrackline }
        --ofile '${ outfile }'

        ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
            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=5.0 (--cutoff)"/>
        <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>

9:acbd3fb47f90

        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgpeakcall
        --ifile '${ infile }'
        --cutoff '${ cutoff }'
        --min-length '${ minlen }'
        --max-gap '${ maxgap }'
        ${ cutoff_analysis } 
        ${ notrackline }
        --ofile '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
            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=5.0 (--cutoff)"/>
        <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>