Mercurial > repos > devteam > vcfbreakcreatemulti
view vcfbreakcreatemulti.xml @ 0:f0dae4ac267e draft
Uploaded
author | devteam |
---|---|
date | Thu, 19 Mar 2015 12:43:19 -0400 |
parents | |
children | 3aa04b92957f |
line wrap: on
line source
<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3"> <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="stdio" /> <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> <expand macro="citations" /> </tool>