comparison vcfbreakcreatemulti.xml @ 0:c0387293312e

Imported from capsule None
author anton
date Wed, 11 Jun 2014 17:11:07 -0400
parents
children 0ffd38828753
comparison
equal deleted inserted replaced
-1:000000000000 0:c0387293312e
1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.1">
2 <requirements>
3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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>