Mercurial > repos > devteam > vcfbreakcreatemulti
comparison vcfbreakcreatemulti.xml @ 0:f0dae4ac267e draft
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| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 12:43:19 -0400 |
| parents | |
| children | 3aa04b92957f |
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| -1:000000000000 | 0:f0dae4ac267e |
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| 1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3"> | |
| 2 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"></expand> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 | |
| 10 #if str($break_or_create) == "break": | |
| 11 vcfbreakmulti "${input1}" > "${out_file1}" | |
| 12 #elif str($break_or_create) == "create": | |
| 13 vcfcreatemulti "${input1}" > "${out_file1}" | |
| 14 #end if | |
| 15 | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> | |
| 20 <param name="break_or_create" type="select" display="radio" label="Break or Create?"> | |
| 21 <option value="break">Break</option> | |
| 22 <option value="create">Create</option> | |
| 23 </param> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="vcf" name="out_file1" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="break_or_create" value="break"/> | |
| 31 <param name="input1" value="vcflib.vcf"/> | |
| 32 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> | |
| 33 </test> | |
| 34 <test> | |
| 35 <param name="break_or_create" value="create"/> | |
| 36 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> | |
| 37 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help> | |
| 41 | |
| 42 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): | |
| 43 | |
| 44 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. | |
| 45 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. | |
| 46 | |
| 47 ---- | |
| 48 | |
| 49 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 50 | |
| 51 </help> | |
| 52 <expand macro="citations" /> | |
| 53 </tool> |