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

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<macros>
    <xml name="BaseRecalibratorParameters" tokens="tag">
        
        <expand macro="macro_bam_input" tag="@TAG@" />

        <param name="knownSites" type="data" format="vcf,bcf,bed,pileup,tabular,table" label="Database of known Sites (ROD files; e.g. VCF format)" multiple="true" title="A database of known polymorphic sites to skip over in the recalibration algorithm" help="-knownSites,&#8209;&#8209;knownSites &amp;lt;knownSites&amp;gt;" />

    </xml>

    <xml name="BaseRecalibratorOutput">
        <data format="tabular" name="br_table" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (Table)">
            <yield />
        </data>
    </xml>

    <template name="BaseRecalibratorPreprocessing">
<![CDATA[
        @token_bam_input_pre@
        #for $i, $variant in enumerate($analysis_type.knownSites):
            ln -s -f ${variant} variant_${i}.vcf &&
        #end for
]]>
    </template>

    <template name="BaseRecalibratorOptions">
<![CDATA[
        --out                   ${br_table}

        @token_bam_input@

        #for $i, $variant in enumerate($analysis_type.knownSites):
            --knownSites variant_${i}.vcf
        #end for
]]>
    </template>
</macros>