view GATK/gatk/analyze_covariates.xml @ 2:2c7824a8d764 draft

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<macros>
    <xml name="AnalyzeCovariatesParameters" tokens="tag">

        <!-- BQSR in main config -->

        <param name="afterReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR second-pass report file" help="-after,&#8209;&#8209;afterReportFile &amp;lt;afterReportFile&amp;gt;" />

        <param name="beforeReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR first-pass report file" help="-before,&#8209;&#8209;beforeReportFile &amp;lt;beforeReportFile&amp;gt;" />

    </xml>

    <xml name="AnalyzeCovariatesOutput">
        <data format="pdf" name="ac_plotsReportFile" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (PDF Recalibration Report)">
            <yield />
        </data>
    </xml>

    <template name="AnalyzeCovariatesPreprocessing">
<![CDATA[
]]>
    </template>

    <template name="AnalyzeCovariatesOptions">
<![CDATA[
        --plotsReportFile                   ${ac_plotsReportFile}

        #if str($analysis_type.afterReportFile)
            --afterReportFile $analysis_type.afterReportFile
        #end if
        #if str($analysis_type.beforeReportFile)
            --beforeReportFile $analysis_type.beforeReportFile
        #end if
]]>
    </template>
</macros>