<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3">
  <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
    <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
    <param name="tag_option" size="20" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
 <tests>
    <test>
      <param name="tag_option" value="added-genotypes"/>
      <param name="input1" value="vcflib.vcf"/>
      <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
      <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
    </test>
    </tests>
<help>

Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation.  Also adds a 'has\_variant' flag for sites where the second file has a variant.

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