annotate genotype_gvcfs.xml @ 0:b80ff7f43ad1 draft default tip

planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty

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

        <expand macro="macro_optional_parameters">


            <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,&#8209;&#8209;sample_ploidy &amp;lt;sample_ploidy&amp;gt;" />

        </expand>

    </xml>

    <xml name="GenotypeGVCFsOutput">
        <data format="vcf" name="gg_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (gVCF)">
            <yield />
        </data>
    </xml>

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

    <template name="GenotypeGVCFsOptions">
<![CDATA[
        --out output.g.vcf

        @token_gvcf_input@

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


</macros>