view vcfbreakcreatemulti.xml @ 2:20eb11864500

Updated tool version to 0.0.2
author Anton Nekrutenko <>
date Wed, 25 Jun 2014 16:36:21 -0400
parents 0ffd38828753
children c5df11927f91
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<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.2">
    <requirement type="package" version="86723982aa">vcflib</requirement>
  <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>

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


    <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>
    <data format="vcf" name="out_file1" />
      <param name="break_or_create" value="break"/>
      <param name="input1" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
      <param name="break_or_create" value="create"/>
      <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
      <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>

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 (