comparison mismatch_profile.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_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@">
    <description>
     calculates the distribution of mismatches across reads
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        mismatch_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq}
        ]]>
    </command>

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

    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="readlength" value="101" />
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
            <output name="outputxls" file="output.mismatch_profile.xls"/>
            <output name="outputr" file="output.mismatch_profile_r"/>
        </test>

60:1421603cc95b

<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
     calculates the distribution of mismatches across reads
    </description>
    <expand macro="bio_tools"/>
    <macros>

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
        ]]>
    </command>

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

    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="read_align_length" value="101" />
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" />
            <output name="outputxls" file="output.mismatch_profile.xls"/>
            <output name="outputr" file="output.mismatch_profile_r"/>
        </test>