Mercurial > repos > anton > vcfselectsamples
annotate vcfselectsamples.xml @ 3:acad111c2466 draft default tip
Uploaded
author | anton |
---|---|
date | Mon, 15 Sep 2014 14:53:50 -0400 |
parents | ca345cfe7119 |
children |
rev | line source |
---|---|
2
ca345cfe7119
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
1
diff
changeset
|
1 <tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.2"> |
0 | 2 <requirements> |
3 | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
0 | 4 </requirements> |
5 <description>Select samples from a VCF dataset</description> | |
6 <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command> | |
7 <inputs> | |
8 <param format="vcf" name="input1" type="data" label="Select VCF dataset" /> | |
9 <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true"> | |
10 <options> | |
11 <filter type="data_meta" ref="input1" key="sample_names" /> | |
12 </options> | |
13 </param> | |
14 </inputs> | |
15 <outputs> | |
16 <data format="vcf" name="out_file1" /> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="vcf_samples" value="NA00001,NA00003"/> | |
21 <param name="input1" value="vcflib.vcf"/> | |
22 <output name="out_file1" file="vcfselectsamples-test1.vcf"/> | |
23 </test> | |
24 </tests> | |
25 <help> | |
26 | |
27 Allows to keep or remove samples from a VCF file. | |
28 | |
29 ----- | |
30 | |
31 .. class:: infomark | |
32 | |
33 | |
34 **Example**: | |
35 | |
36 Selecting *NA00001* and *NA00003* from the following VCF line:: | |
37 | |
38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | |
39 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:.,. | |
40 | |
41 will, obviously, remove *NA00002*:: | |
42 | |
43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 | |
44 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:.,. | |
45 | |
46 ---- | |
47 | |
48 Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
49 | |
50 | |
51 | |
52 | |
53 </help> | |
54 </tool> |