gatk4_gathervcfs.xml

<?xml version="1.0"?>
<tool id="gatk4_gathervcfs" name="GATK4 GatherVcfs (Picard)" version="@WRAPPER_VERSION@0" profile="17.09">

    <description>- Gathers multiple VCF files from a scatter operation into a single VCF file</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="version_cmd"/>

    <command detect_errors="exit_code"><![CDATA[
        #include source=$vcf_tabix#

        @CMD_BEGIN@ GatherVcfs
        
        #include source=$picard_opts#
        #include source=$picard_vcf_output_opts#
        #include source=$vcf_input#
        #include source=$picard_ref_opts#

    ]]></command>

    <inputs>
        <expand macro="picard_vcf_params" />
        <param name="input" argument="--INPUT" type="data" optional="false" format="vcf,vcf_bgzip" label="Input" help="Input VCF file(s)." />
        <section name="optional" title="Optional Parameters" expanded="False">

            <expand macro="ref_sel" />
        </section>
        <expand macro="picard_params" />
    </inputs>

    <outputs>
        <expand macro="picard_vcf_output_params" />
        <expand macro="picard_output_params" />

    </outputs>

    <tests>
    </tests>

    <help><![CDATA[
    Simple little class that combines multiple VCFs that have exactly the
same set of samples and totally discrete sets of loci.

    ]]></help>

    <expand macro="citations"/>

</tool>