comparison macs2_predictd.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 predictd

        -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
        @tag_size@
        @effective_genome_size@

        > '${ outfile }'

        &&

        Rscript predictd
        ]]>
    </command>
    <inputs>
        <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
               label="ChIP-seq alignment file"
               help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
        <expand macro="conditional_effective_genome_size" />

            <param name="gsize" value="3300000000" />
            <param name="tsize" value=""/>
            <param name="band_width" value="300"/>
            <param name="lower" value="5"/>
            <param name="upper" value="50"/>
            <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help>
<![CDATA[

9:acbd3fb47f90

        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 predictd

        -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
        @tag_size@
        @effective_genome_size@

        > '${ outfile }'

        &&

        Rscript predictd
    ]]></command>
    <inputs>
        <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
               label="ChIP-seq alignment file"
               help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
        <expand macro="conditional_effective_genome_size" />

            <param name="gsize" value="3300000000" />
            <param name="tsize" value=""/>
            <param name="band_width" value="300"/>
            <param name="lower" value="5"/>
            <param name="upper" value="50"/>
            <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt" lines_diff="2"/>
            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help>
<![CDATA[