comparison vcfbreakcreatemulti.xml @ 0:f0dae4ac267e draft

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author devteam
date Thu, 19 Mar 2015 12:43:19 -0400
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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>