comparison geneBody_coverage2.xml @ 59:dbedfc5f5a3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"

58:1a052c827e88

<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@WRAPPER_VERSION@.1">
    <description>
        Read coverage over gene body
    </description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    </command>

    <inputs>
        <param name="input" type="data" label="Input bigwig file" format="bigwig" />
        <expand macro="refgene_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
        <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
        <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
            <output name="outputr" file="output.geneBodyCoverage2.r" />
            <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
        </test>
    </tests>

    <help><![CDATA[

59:dbedfc5f5a3c

<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@.2">
    <description>
        Read coverage over gene body
    </description>
    <expand macro="bio_tools"/>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    </command>

    <inputs>
        <param name="input" type="data" label="Input bigwig file" format="bigwig" />
        <expand macro="refgene_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
        <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
        <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
    </outputs>

    <tests>
        <test expect_num_outputs="3">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
            <output name="outputr" file="output.geneBodyCoverage2_r" />
            <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
        </test>
    </tests>

    <help><![CDATA[