comparison RNA_fragment_size.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_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@.1">
    <description>
     calculates the fragment size for each gene/transcript
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        ln -sf '${input}' 'input.bam' &&
        ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
        RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />

60:1421603cc95b

<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
     calculates the fragment size for each gene/transcript
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />