Mercurial > repos > devteam > vcftools_isec
comparison vcftools_isec.xml @ 0:799feac145c8 draft
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| author | devteam |
|---|---|
| date | Sun, 24 Nov 2013 11:12:03 -0500 |
| parents | |
| children | 9e576efe7836 |
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| -1:000000000000 | 0:799feac145c8 |
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| 1 <tool id="vcftools_isec" name="Intersect" version="0.1"> | |
| 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> | |
| 8 | |
| 9 <command> | |
| 10 ## Preprocessing for each dataset. | |
| 11 #set dataset_names = [] | |
| 12 #for i, $input in enumerate( $inputs ): | |
| 13 ## Sort file. | |
| 14 vcf-sort ${input.file} > ${i}.vcf.sorted ; | |
| 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 | |
| 29 #end if | |
| 30 #echo ' '.join( dataset_names ) # > ${output} | |
| 31 </command> | |
| 32 <inputs> | |
| 33 <repeat name="inputs" title="Dataset" min="2"> | |
| 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"/> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data name="output" format="vcf"/> | |
| 41 </outputs> | |
| 42 | |
| 43 <stdio> | |
| 44 <regex match=".*" source="both" level="log" description="tool progress"/> | |
| 45 </stdio> | |
| 46 | |
| 47 <tests> | |
| 48 <!-- Cannot specify multiple repeats in test framework right now. | |
| 49 <test> | |
| 50 <param name='inputs|1' value='1.vcf' /> | |
| 51 <param name='inputs|2' value='2.vcf' /> | |
| 52 <param name='complement' value='False' /> | |
| 53 <output name='output' file='out.vcf' /> | |
| 54 </test> | |
| 55 --> | |
| 56 </tests> | |
| 57 | |
| 58 <help> | |
| 59 Please see the VCFtools `documentation`__ for help and further information. | |
| 60 | |
| 61 .. __: http://vcftools.sourceforge.net/docs.html | |
| 62 </help> | |
| 63 </tool> |