<tool id="vcffixup" name="VCFfixup:" version="0.0.3">
  <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <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 selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.

----

Vcffixup @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>