comparison bam2wig.xml @ 60:1421603cc95b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d

59:dbedfc5f5a3c

<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@">
    <description>
        converts all types of RNA-seq data from .bam to .wig
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

    <version_command><![CDATA[bam2wig.py --version]]></version_command>

    <command><![CDATA[
        ln -sf '${input}' 'input.bam' &&
        ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
        bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile

        #if str($strand_type.strand_specific) == "pair"
            -d
            #if str($strand_type.pair_type) == "sd"
                '1++,1--,2+-,2-+'

60:1421603cc95b

<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
        converts all types of RNA-seq data from .bam to .wig
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

    <version_command><![CDATA[bam2wig.py --version]]></version_command>

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile

        #if str($strand_type.strand_specific) == "pair"
            -d
            #if str($strand_type.pair_type) == "sd"
                '1++,1--,2+-,2-+'