Mercurial > repos > devteam > vcfselectsamples
comparison vcfselectsamples.xml @ 0:88fd8ef7e4af draft
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| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 14:45:17 -0400 |
| parents | |
| children | 43cecdfe7107 |
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| -1:000000000000 | 0:88fd8ef7e4af |
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| 1 <tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.3"> | |
| 2 <description>Select samples from a VCF dataset</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"></expand> | |
| 7 <expand macro="stdio" /> | |
| 8 <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command> | |
| 9 <inputs> | |
| 10 <param format="vcf" name="input1" type="data" label="Select VCF dataset" /> | |
| 11 <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true"> | |
| 12 <options> | |
| 13 <filter type="data_meta" ref="input1" key="sample_names" /> | |
| 14 </options> | |
| 15 </param> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="vcf" name="out_file1" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="vcf_samples" value="NA00001,NA00003"/> | |
| 23 <param name="input1" value="vcflib.vcf"/> | |
| 24 <output name="out_file1" file="vcfselectsamples-test1.vcf"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 | |
| 29 Allows to keep or remove samples from a VCF file. | |
| 30 | |
| 31 ----- | |
| 32 | |
| 33 .. class:: infomark | |
| 34 | |
| 35 | |
| 36 **Example**: | |
| 37 | |
| 38 Selecting *NA00001* and *NA00003* from the following VCF line:: | |
| 39 | |
| 40 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | |
| 41 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. | |
| 42 | |
| 43 will, obviously, remove *NA00002*:: | |
| 44 | |
| 45 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 | |
| 46 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. | |
| 47 | |
| 48 ---- | |
| 49 | |
| 50 Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 51 </help> | |
| 52 <expand macro="citations" /> | |
| 53 </tool> |