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comparison vcftools_merge.xml @ 2:60743b92cc26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:35:52 -0500
parents eb02907453b4
children
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1:eb02907453b4 2:60743b92cc26
1 <tool id="vcftools_merge" name="Merge" version="0.1"> 1 <tool id="vcftools_merge" name="Merge" 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.
23 #end for 23 #end for
24 24
25 ## Merge. 25 ## Merge.
26 vcf-merge 26 vcf-merge
27 #echo ' '.join( dataset_names ) # > ${output} 27 #echo ' '.join( dataset_names ) # > ${output}
28 28
29 </command> 29 </command>
30 <inputs> 30 <inputs>
31 <repeat name="inputs" title="Datasets to Merge" min="2"> 31 <param name="input_files" label="Datasets to Merge" type="data" format="vcf" min="2" multiple="True"/>
32 <param name="file" label="Dataset" type="data" format="vcf"/>
33 </repeat>
34 </inputs> 32 </inputs>
35 33
36 <outputs> 34 <outputs>
37 <data name="output" format="vcf"/> 35 <data name="output" format="vcf"/>
38 </outputs> 36 </outputs>