annotate ngsap-vc/gatk/combine_gvcfs.xml @ 3:0d10255b5434 draft default tip

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<macros>
    <xml name="CombineGVCFsParameters" tokens="tag">
        
        <expand macro="macro_gvcf_input" tag="@TAG@" />

        <expand macro="macro_optional_parameters">

            <param name="breakBandsAtMultiplesOf" type="integer" value="0" label="If > 0, reference bands will be broken up at genomic positions that are multiples of this number" help="-breakBandsAtMultiplesOf,&#8209;&#8209;breakBandsAtMultiplesOf &amp;lt;breakBandsAtMultiplesOf&amp;gt;" />

        </expand>

    </xml>

    <xml name="CombineGVCFsOutput">
        <data format="vcf" name="cg_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
            <yield />
        </data>
    </xml>

    <template name="CombineGVCFsPreprocessing">
<![CDATA[
        @token_gvcf_input_pre@
]]>
    </template>

    <template name="CombineGVCFsOptions">
<![CDATA[
        --out ${cg_output_vcf}

        @token_gvcf_input@

        #set $optionals = $analysis_type.optional_parameters
        #if $optionals.optional_parameters_enabled
            #if $optionals.breakBandsAtMultiplesOf > 0
                --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf
            #end if
        #end if
]]>
    </template>


</macros>