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

        <conditional name="cond_usage">
            <param name="cond_usage_selector" type="select" label="Select usage">
                <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option>
            </param>
            <when value="GVCF">
                <expand macro="HaplotypeCallerGVCF" />
            </when>
        </conditional>

        <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="HaplotypeCallerOutput">
        <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)">
            <yield />
        </data>
    </xml>

    <template name="HaplotypeCallerPreprocessing">
<![CDATA[
        @token_bam_input_pre@
]]>
    </template>

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

        @token_bam_input@

        #set $optionals = $analysis_type.optional_parameters
        #if $optionals.optional_parameters_enabled
            --sample_ploidy $optionals.sample_ploidy
        #end if

        #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector
        #set $usage = $analysis_type.cond_usage

        #if str($usage_selector) == 'GVCF'
            --emitRefConfidence "GVCF"
        #end if
]]>
    </template>



    <xml name="HaplotypeCallerGVCF">
        <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &amp;lt;emitRefConfidence&amp;gt;">
              <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option>
        </param>
    </xml>

</macros>