<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.2">
<requirements>
    <requirement type="package" version="8a5602bf07">vcflib</requirement>
</requirements>
  <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
  <command>

   #if str($break_or_create) == "break":
       vcfbreakmulti "${input1}" > "${out_file1}"
   #elif str($break_or_create) == "create": 
       vcfcreatemulti "${input1}" > "${out_file1}"
   #end if

</command>

  <inputs>
    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
    <param name="break_or_create" type="select" display="radio" label="Break or Create?">
      <option value="break">Break</option>
      <option value="create">Create</option>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="break_or_create" value="break"/>
      <param name="input1" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
    </test>
    <test>
      <param name="break_or_create" value="create"/>
      <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
      <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
    </test>
  </tests>
  <help>

This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):

 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.

----

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

</help>
</tool>