Mercurial > repos > anton > vcfselectsamples
diff vcfselectsamples.xml @ 0:41f097b3d55a
Imported from capsule None
author | anton |
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date | Wed, 11 Jun 2014 17:11:51 -0400 |
parents | |
children | d1ede06c0b29 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfselectsamples.xml Wed Jun 11 17:11:51 2014 -0400 @@ -0,0 +1,54 @@ +<tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.1"> +<requirements> + <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> +</requirements> + <description>Select samples from a VCF dataset</description> + <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset" /> + <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true"> + <options> + <filter type="data_meta" ref="input1" key="sample_names" /> + </options> +</param> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="vcf_samples" value="NA00001,NA00003"/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfselectsamples-test1.vcf"/> + </test> + </tests> + <help> + +Allows to keep or remove samples from a VCF file. + +----- + +.. class:: infomark + + +**Example**: + +Selecting *NA00001* and *NA00003* from the following VCF line:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 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:.,. + +will, obviously, remove *NA00002*:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 + 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:.,. + +---- + +Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + + + + +</help> +</tool>