Mercurial > repos > devteam > vcfbreakcreatemulti
comparison vcfbreakcreatemulti.xml @ 0:f0dae4ac267e draft
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author | devteam |
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date | Thu, 19 Mar 2015 12:43:19 -0400 |
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children | 3aa04b92957f |
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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> |