<tool id="vcfcombine" name="VCFcombine:" version="0.0.3">
  <description>Combine multiple VCF datasets</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>

   vcfcombine
   
   #for $input_vcf in $input_vcfs:
        "${input_vcf.input_vcf}"
   #end for

   > "${out_file1}"

  </command>
  <inputs>
    <repeat name="input_vcfs" title="Select VCF dataset" min="2" >
      <param name="input_vcf" type="data" format="vcf" label="Dataset"/>
    </repeat>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input_vcf" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfcombine-test1.vcf"/>
    </test>
    </tests>
  <help>

Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted.

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