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view tools/qualimap_parser/qualimap_parser.xml @ 0:45533fb9d2f4 draft default tip

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author matnguyen
date Tue, 04 Sep 2018 02:49:49 -0400
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<tool id="parse_qualimap" name="Parse Qualimap reports" version="0.1.0">
    <description>and output a list of outliers</description>
    <command><![CDATA[
        $__tool_directory__/qualimap_parser -n #for $report in $reports# ${report.element_identifier} #end for#
        -i #for $report in $reports# $report #end for#
    ]]></command>
    <inputs>
        <param name="reports" type="data" format="txt" label="Qualimap Genome Report" help="" optional="false" multiple="True" />
    </inputs>
    <outputs>
        <data name="output_file" label="Outliers from dataset after mapping" format="txt" from_work_dir="outlier_list.txt"/>
    </outputs>

    <tests>
        <test>

        </test>
    </tests>

    <help><![CDATA[
    Parses Qualimap reports and outputs a list of outliers based on percentage of the reference genome covered and mean mapping quality.

    Command line:
    qualimap_parser -n <accessions> -i <reports>

    ]]></help>

    <citations>
        Manuscript in preparation
    </citations>
</tool>