Mercurial > repos > devteam > vcftools_isec
annotate vcftools_isec.xml @ 1:aa232e38338f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 13:02:25 -0500 |
parents | 026d0f104183 |
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aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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1 <tool id="vcftools_isec" name="Intersect" version="0.1.1"> |
0 | 2 <description>multiple VCF datasets</description> |
3 | |
4 <requirements> | |
5 <requirement type="package">tabix</requirement> | |
6 <requirement type="package" version="0.1.11">vcftools</requirement> | |
7 </requirements> | |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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8 |
0 | 9 <command> |
10 ## Preprocessing for each dataset. | |
11 #set dataset_names = [] | |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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12 #for i, $input in enumerate( $input_files ): |
0 | 13 ## Sort file. |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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14 vcf-sort ${input} > ${i}.vcf.sorted ; |
0 | 15 |
16 ## Compress. | |
17 bgzip ${i}.vcf.sorted ; | |
18 | |
19 ## Index. | |
20 tabix -p vcf ${i}.vcf.sorted.gz ; | |
21 | |
22 #silent dataset_names.append( str($i) + '.vcf.sorted.gz' ) | |
23 #end for | |
24 | |
25 ## Intersect. | |
26 vcf-isec -f | |
27 #if $complement: | |
28 -c | |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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29 #end if |
0 | 30 #echo ' '.join( dataset_names ) # > ${output} |
31 </command> | |
32 <inputs> | |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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33 <param name="input_files" label="Datasets" type="data" format="vcf" min="2" multiple="True"/> |
0 | 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"/> |
35 </inputs> | |
36 | |
37 <outputs> | |
38 <data name="output" format="vcf"/> | |
39 </outputs> | |
40 | |
41 <stdio> | |
42 <regex match=".*" source="both" level="log" description="tool progress"/> | |
43 </stdio> | |
44 | |
45 <tests> | |
46 <!-- Cannot specify multiple repeats in test framework right now. | |
47 <test> | |
1
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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48 <param name='input_files|1' value='1.vcf' /> |
aa232e38338f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
49 <param name='input_files|2' value='2.vcf' /> |
0 | 50 <param name='complement' value='False' /> |
51 <output name='output' file='out.vcf' /> | |
52 </test> | |
53 --> | |
54 </tests> | |
55 | |
56 <help> | |
57 Please see the VCFtools `documentation`__ for help and further information. | |
58 | |
59 .. __: http://vcftools.sourceforge.net/docs.html | |
60 </help> | |
61 </tool> |