<tool id="vcf_annotate" name="Annotate" version="1.0.0">
  <description>a VCF file (dbSNP, hapmap)</description>
  <command interpreter="python">
    vcfPytools.py
      annotate 
      --in=$input1
      #if $annotation_options.annotate == "dbsnp"
      --dbsnp=$input2
      #elif $annotation_options.annotate == "hapmap"
      --hapmap=$input2
      #end if
      --out=$output1
  </command>
  <inputs>
    <param name="input1" label="VCF file to annotate" type="data" format="vcf" />
    <conditional name="annotation_options">
      <param name="annotate" type="select" label="annotation source">
        <option value="dbsnp">dbSNP vcf file</option>
        <option value="hapmap">hapmap vcf file</option>
      </param>
      <when value="dbsnp">
        <param name="input2" label="dbSNP vcf file" type="data" format="vcf" help="This option will annotate the vcf file with dbSNP rsid values.  The input dbSNP file must also be in vcf v4.0 format.  Only dbSNP entries with VC=SNP are included."/>
      </when>
      <when value="hapmap">
        <param name="input2" label="hapmap vcf file" type="data" format="vcf" help="This option will annotate the vcf file info string to include HM3 if the record is included hapmap.  If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A."/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="vcf" name="output1" label="${tool.name} ${on_string}" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="test.small.vcf" ftype="vcf" />
      <param name="annotate" value="dbsnp" />
      <param name="input2" value="dbsnp.small.vcf" ftype="vcf" />
      <output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" />
    </test>
    <test>
      <param name="input1" value="test.small.vcf" ftype="vcf" />
      <param name="annotate" value="hapmap" />
      <param name="input2" value="hapmap.small.vcf" ftype="vcf" />
      <output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" />
    </test>
  </tests>
  <help>

**What it does**

This tool uses vcfPytools_' annotate command annotate a VCF file

.. _vcfPytools: https://github.com/AlistairNWard/vcfPytools

Currently, either a hapmap or a dbsnp file should be provided, not both.

dbSNP option will annotate the VCF file with dbSNP rsid values.  The input dbSNP file must also be in VCF v4.0 format.  Only dbSNP entries with VC=SNP are included.

hapmap option will annotate the VCF file info string to include HM3 if the record is included hapmap.  If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A.


  </help>
</tool>