annotate GATK/gatk/realigner_target_creator.xml @ 2:2c7824a8d764 draft

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

        <expand macro="macro_optional_parameters">
            <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,&#8209;&#8209;maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
            <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,&#8209;&#8209;minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
            <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,&#8209;&#8209;windowSize &amp;lt;windowSize&amp;gt;" />

            <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,&#8209;&#8209;mismatchFraction &amp;lt;mismatchFraction&amp;gt;" />
            <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,&#8209;&#8209;known &amp;lt;known&amp;gt;">
                <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
            </repeat>
        </expand>
        
    </xml>

    <xml name="RealignerTargetCreatorOutput">
        <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)">
            <yield />
        </data>
    </xml>

    <template name="RealignerTargetCreatorPreprocessing">
<![CDATA[
        @token_bam_input_pre@

        #if $analysis_type.optional_parameters.optional_parameters_enabled
            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
                ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf &&
            #end for
        #end if
]]>
    </template>

    <template name="RealignerTargetCreatorOptions">
<![CDATA[
        --out                   ${rtc_output_intervals}

        @token_bam_input@

        #if $analysis_type.optional_parameters.optional_parameters_enabled
            --maxIntervalSize       ${analysis_type.optional_parameters.maxIntervalSize}
            --minReadsAtLocus       ${analysis_type.optional_parameters.minReadsAtLocus}
            --windowSize            ${analysis_type.optional_parameters.windowSize}
            --mismatchFraction      ${analysis_type.optional_parameters.mismatchFraction}

            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
                --known rod_binding_${i}.vcf
            #end for
        #end if
]]>
    </template>
</macros>