Mercurial > repos > anton > vcfbreakcreatemulti
annotate vcfbreakcreatemulti.xml @ 1:0ffd38828753
Updated to vcflib 86723982aa
| author | Anton Nekrutenko <anton@bx.psu.edu> |
|---|---|
| date | Wed, 25 Jun 2014 16:12:20 -0400 |
| parents | c0387293312e |
| children | 20eb11864500 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.1"> |
| 2 <requirements> | |
|
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0ffd38828753
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
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changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> | |
| 6 <command> | |
| 7 | |
| 8 #if str($break_or_create) == "break": | |
| 9 vcfbreakmulti "${input1}" > "${out_file1}" | |
| 10 #elif str($break_or_create) == "create": | |
| 11 vcfcreatemulti "${input1}" > "${out_file1}" | |
| 12 #end if | |
| 13 | |
| 14 </command> | |
| 15 | |
| 16 <inputs> | |
| 17 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> | |
| 18 <param name="break_or_create" type="select" display="radio" label="Break or Create?"> | |
| 19 <option value="break">Break</option> | |
| 20 <option value="create">Create</option> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="vcf" name="out_file1" /> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="break_or_create" value="break"/> | |
| 29 <param name="input1" value="vcflib.vcf"/> | |
| 30 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> | |
| 31 </test> | |
| 32 <test> | |
| 33 <param name="break_or_create" value="create"/> | |
| 34 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> | |
| 35 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
| 39 | |
| 40 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): | |
| 41 | |
| 42 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. | |
| 43 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. | |
| 44 | |
| 45 ---- | |
| 46 | |
| 47 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 48 | |
| 49 </help> | |
| 50 </tool> |