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comparison vcfbreakcreatemulti.xml @ 1:cf6b34535a33 draft default tip

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author anton
date Tue, 10 Jun 2014 12:12:37 -0400
parents 448b21afcafa
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1 <tool id="vcfbreakcreatemulti" name="VCF-Break-Create-multi:" version="0.0.1"> 1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
4 </requirements> 4 </requirements>
5 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> 5 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
6 <command> 6 <command>
12 #end if 12 #end if
13 13
14 </command> 14 </command>
15 15
16 <inputs> 16 <inputs>
17 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
17 <param name="break_or_create" type="select" display="radio" label="Break or Create?"> 18 <param name="break_or_create" type="select" display="radio" label="Break or Create?">
18 <option value="break">Break</option> 19 <option value="break">Break</option>
19 <option value="create">Create</option> 20 <option value="create">Create</option>
20 </param> 21 </param>
21 <param format="vcf" name="input1" type="data" label="In this VCF dataset"/>
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <data format="vcf" name="out_file1" /> 24 <data format="vcf" name="out_file1" />
25 </outputs> 25 </outputs>
26 <tests> 26 <tests>
35 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> 35 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
36 </test> 36 </test>
37 </tests> 37 </tests>
38 <help> 38 <help>
39 39
40 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively). 40 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
41 41
42 - Breaking = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. 42 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
43 - Creation = If overlapping alleles are represented across multiple records, merge them into a single record. 43 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
44 44
45 ---- 45 ----
46 46
47 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 47 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
48 48