comparison FPKM_count.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_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@.1">
    <description>calculates raw read count, FPM, and FPKM for each gene</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        ln -sf '${input}' 'local_input.bam' &&
        ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' &&
        FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'

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

60:1421603cc95b

<tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>calculates raw read count, FPM, and FPKM for each gene</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'

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