comparison macs2_predictd.xml @ 2:bfe57d6e0c4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74

1:859c982b1f7f

<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
    <description>Predict 'd' or fragment size from alignment results</description>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
    </expand>
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 predictd
            -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
            @tag_size@
            @effective_genome_size@

            ## remove the timepoint and strip the output
            2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'

            > "${ outfile }"
            
        &&

        Rscript predictd
    </command>
    <expand macro="stdio" />
    <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" />
        <expand macro="tag_size" />
        <expand macro="band_width" />

2:bfe57d6e0c4c

<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
    <description>Predict 'd' or fragment size from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        macs2 predictd
            -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
            @tag_size@
            @effective_genome_size@

            ## remove the timepoint and strip the output
            2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'

            > "${ 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" />
        <expand macro="tag_size" />
        <expand macro="band_width" />