vcf-filter.xml

<tool id="vcf-filter" name="VCF Filter" version="0.1">
    <description></description>

    <requirements>
        <container type="docker">tcgavcf-tool:0.1</container>
    </requirements>

    <command interpreter="python">
vcf-filter.py ${input_vcf} ${filter} ${output_vcf}
#if $filterRejects:
--filter
#end if
    </command>

    <inputs>
        <param type="data" format="vcf" name="input_vcf" label="Input VCF"/>
        <param type="text" area="True" size="5x25" name="filter_text" label="Allowed Sequences"/>
        <param name="filterRejects" type="boolean" label="Filter Rejected calls" checked="true"/>
    </inputs>

    <outputs>
        <data format="vcf" name="output_vcf" />
    </outputs>
    <configfiles>
        <configfile name="filter"><![CDATA[${filter_text}]]></configfile>
    </configfiles>
    <help>

    </help>

    <tests>
    </tests>

</tool>