<tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3">
  <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>

   #if str($analysis_type) == "count":
       vcfhetcount "${vcf_input}" > "${out_file1}"
   #elif str($analysis_type) == "ratio": 
       vcfhethomratio "${vcf_input}" > "${out_file1}"
   #elif str($analysis_type) == "allele_count":
       vcfcountalleles "${vcf_input}" > "${out_file1}" 
   #end if

</command>

  <inputs>
    <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
      <option value="count">Compute the number of heterozygotes</option>
      <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
      <option value="allele_count">Compute the total number of alleles</option>
    </param>
    <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="analysis_type" value="count"/>
      <param name="vcf_input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfhethom-test1.tab"/>
    </test>
    <test>
      <param name="analysis_type" value="ratio"/>
      <param name="vcf_input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfhethom-test2.tab"/>
    </test>
    <test>
      <param name="analysis_type" value="allele_count"/>
      <param name="vcf_input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfhethom-test3.tab"/>
    </test>
  </tests>
  <help>

This tool performs three basic calculations: 

(1) Computes the number of heterozygotes
(2) Computes the ratio between heterozygotes and homozygotes
(3) Computes the total number of alleles in the input dataset

----

This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 

</help>
  <expand macro="citations" />
</tool>