<tool id="vcffixup" name="VCFfixup:" version="0.0.1">
<requirements>
    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
</requirements>
  <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
  <command>vcffixup "${input1}" > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="vcflib.vcf"/>
      <output name="out_file1" file="vcffixup-test1.vcf"/>
    </test>
    </tests>
  <help>

Uses genotypes from the VCF file to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.

----

Vcffixup is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 

</help>
</tool>