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comparison vcfbreakcreatemulti.xml @ 1:3aa04b92957f draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:04:07 -0400
parents f0dae4ac267e
children 690b1d846263
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0:f0dae4ac267e 1:3aa04b92957f
1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3"> 1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@.0">
2 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> 2 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 9 #if str($break_or_create) == "break":
10 #if str($break_or_create) == "break": 10 vcfbreakmulti "${input1}" > "${out_file1}"
11 vcfbreakmulti "${input1}" > "${out_file1}" 11 #elif str($break_or_create) == "create":
12 #elif str($break_or_create) == "create": 12 vcfcreatemulti "${input1}" > "${out_file1}"
13 vcfcreatemulti "${input1}" > "${out_file1}" 13 #end if
14 #end if 14 </command>
15 15 <inputs>
16 </command> 16 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
17 17 <param name="break_or_create" type="select" display="radio" label="Break or Create?">
18 <inputs> 18 <option value="break">Break</option>
19 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> 19 <option value="create">Create</option>
20 <param name="break_or_create" type="select" display="radio" label="Break or Create?"> 20 </param>
21 <option value="break">Break</option> 21 </inputs>
22 <option value="create">Create</option> 22 <outputs>
23 </param> 23 <data format="vcf" name="out_file1" />
24 </inputs> 24 </outputs>
25 <outputs> 25 <tests>
26 <data format="vcf" name="out_file1" /> 26 <test>
27 </outputs> 27 <param name="break_or_create" value="break"/>
28 <tests> 28 <param name="input1" value="vcflib.vcf"/>
29 <test> 29 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
30 <param name="break_or_create" value="break"/> 30 </test>
31 <param name="input1" value="vcflib.vcf"/> 31 <test>
32 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> 32 <param name="break_or_create" value="create"/>
33 </test> 33 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
34 <test> 34 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
35 <param name="break_or_create" value="create"/> 35 </test>
36 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> 36 </tests>
37 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> 37 <help>
38 </test>
39 </tests>
40 <help>
41
42 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): 38 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
43 39
44 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. 40 - **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. 41 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
46 42
47 ---- 43 ----
48 44
49 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 45 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
50 46 </help>
51 </help> 47 <expand macro="citations" />
52 <expand macro="citations" />
53 </tool> 48 </tool>