<?xml version="1.0"?>
<tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="@DEFUSE_VERSION@.2">
  <description>generate a VCF from a DeFuse Results file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
  <command interpreter="python">defuse_results_to_vcf.py  --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
  </command>
  <inputs>
    <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> 
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>
    <data name="vcf" metadata_source="defuse_results" format="vcf"/>
  </outputs>
  <tests>
    <test>
      <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
      <output name="vcf" file="mm10_results.filtered.vcf"/>
    </test>
  </tests>
  <help>
**Defuse Results to VCF**

Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.   

This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.   

.. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
  </help>
</tool>