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comparison vcftools_isec.xml @ 1:9e576efe7836 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:35:37 -0500
parents 799feac145c8
children
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0:799feac145c8 1:9e576efe7836
1 <tool id="vcftools_isec" name="Intersect" version="0.1"> 1 <tool id="vcftools_isec" name="Intersect" version="0.1.1">
2 <description>multiple VCF datasets</description> 2 <description>multiple VCF datasets</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package">tabix</requirement> 5 <requirement type="package">tabix</requirement>
6 <requirement type="package" version="0.1.11">vcftools</requirement> 6 <requirement type="package" version="0.1.11">vcftools</requirement>
7 </requirements> 7 </requirements>
8 8
9 <command> 9 <command>
10 ## Preprocessing for each dataset. 10 ## Preprocessing for each dataset.
11 #set dataset_names = [] 11 #set dataset_names = []
12 #for i, $input in enumerate( $inputs ): 12 #for i, $input in enumerate( $input_files ):
13 ## Sort file. 13 ## Sort file.
14 vcf-sort ${input.file} > ${i}.vcf.sorted ; 14 vcf-sort ${input} > ${i}.vcf.sorted ;
15 15
16 ## Compress. 16 ## Compress.
17 bgzip ${i}.vcf.sorted ; 17 bgzip ${i}.vcf.sorted ;
18 18
19 ## Index. 19 ## Index.
24 24
25 ## Intersect. 25 ## Intersect.
26 vcf-isec -f 26 vcf-isec -f
27 #if $complement: 27 #if $complement:
28 -c 28 -c
29 #end if 29 #end if
30 #echo ' '.join( dataset_names ) # > ${output} 30 #echo ' '.join( dataset_names ) # > ${output}
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <repeat name="inputs" title="Dataset" min="2"> 33 <param name="input_files" label="Datasets" type="data" format="vcf" min="2" multiple="True"/>
34 <param name="file" label="Dataset" type="data" format="vcf"/>
35 </repeat>
36 <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/> 34 <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/>
37 </inputs> 35 </inputs>
38 36
39 <outputs> 37 <outputs>
40 <data name="output" format="vcf"/> 38 <data name="output" format="vcf"/>
45 </stdio> 43 </stdio>
46 44
47 <tests> 45 <tests>
48 <!-- Cannot specify multiple repeats in test framework right now. 46 <!-- Cannot specify multiple repeats in test framework right now.
49 <test> 47 <test>
50 <param name='inputs|1' value='1.vcf' /> 48 <param name='input_files|1' value='1.vcf' />
51 <param name='inputs|2' value='2.vcf' /> 49 <param name='input_files|2' value='2.vcf' />
52 <param name='complement' value='False' /> 50 <param name='complement' value='False' />
53 <output name='output' file='out.vcf' /> 51 <output name='output' file='out.vcf' />
54 </test> 52 </test>
55 --> 53 -->
56 </tests> 54 </tests>