<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="3">
    <description>to tabular hrdetect</description>
    <requirements>
        <requirement type="package" version="0.2.8">smoove</requirement>
    </requirements>
    <macros>
        <import>macro_lumpy_smoove.xml</import>
    </macros>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
    @pipefail@
    python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular'
    ]]></command>
    <inputs>
        <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/>
   </inputs>

    <outputs>
        <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" />
    </outputs>

    <tests>
        <test>
            <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" />
            <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" sort="true" ftype="tabular" />
        </test>
    </tests>
    <help>
**vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with
the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv)
    </help>

    <citations>
    <citation type="doi">10.1038/nm.4292</citation>
  </citations>
</tool>