<tool id="vcfannotate" name="VCFannotate:" version="0.0.3">
  <description>Intersect VCF records with BED annotations</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
  <inputs>        
    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
    <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
    <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
      <param name="key_option" value="BED-features"/>
      <param name="input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
    </test>
    </tests>
  <help>

Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. 

-----

.. class:: infomark


**Example**:

The following VCF line::

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00002      NA00003
 20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                                                                                       FORMAT      NA00001        NA00002      NA00003                                                  
 20     1110696 rs6040355 A   G,T 67   PASS   AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

----

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