Mercurial > repos > devteam > vcf2pgsnp
comparison vcf2pgSnp.xml @ 0:ae1b0fbd53e8 draft default tip
Imported from capsule None
author | devteam |
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date | Mon, 28 Jul 2014 11:30:07 -0400 |
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-1:000000000000 | 0:ae1b0fbd53e8 |
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1 <tool id="vcf2pgSnp" name="VCF to pgSnp" hidden="false" version="1.0.0"> | |
2 <description>Convert from VCF to pgSnp format</description> | |
3 <command interpreter="perl"> | |
4 #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1 | |
5 #else #vcf2pgSnp.pl $inType.ind_column $input1 > $out_file1 | |
6 #end if | |
7 </command> | |
8 <inputs> | |
9 <param format="vcf" name="input1" type="data" label="VCF dataset" /> | |
10 <conditional name="inType"> | |
11 <param name="how" type="select" label="How to treat individuals"> | |
12 <option value="all">Group all as a population</option> | |
13 <option value="one">Do just one individual</option> | |
14 </param> | |
15 <when value="one"> | |
16 <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" /> | |
17 </when> | |
18 <when value="all"> | |
19 <!-- do nothing --> | |
20 </when> | |
21 </conditional> | |
22 </inputs> | |
23 <outputs> | |
24 <data format="interval" name="out_file1" /> | |
25 </outputs> | |
26 <tests> | |
27 <test> | |
28 <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" /> | |
29 <param name="how" value="all" /> | |
30 <output name="output" file="vcf2pgSnp_output.pgSnp" /> | |
31 </test> | |
32 </tests> | |
33 | |
34 <help> | |
35 **Dataset formats** | |
36 | |
37 The input dataset is VCF_ format. | |
38 The output dataset is pgSnp_. (`Dataset missing?`_) | |
39 | |
40 .. _Dataset missing?: ./static/formatHelp.html | |
41 .. _VCF: ./static/formatHelp.html#vcf | |
42 .. _pgSnp: ./static/formatHelp.html#pgSnp | |
43 | |
44 ----- | |
45 | |
46 **What it does** | |
47 | |
48 This converts a VCF dataset to pgSnp with the frequency counts being | |
49 chromosome counts. If there is more than one column of SNP data it will either | |
50 accumulate all columns as a population or convert the column indicated | |
51 to pgSnp. | |
52 | |
53 ----- | |
54 | |
55 **Examples** | |
56 | |
57 - input:: | |
58 | |
59 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48 | |
60 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 | |
61 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48 | |
62 etc. | |
63 | |
64 - output as a population:: | |
65 | |
66 chr1 13326 13327 G/C 2 7,1 0,0 | |
67 chr1 13979 13980 T/C 2 7,1 0,0 | |
68 chr1 30922 30923 G/T 2 4,4 0,0 | |
69 etc. | |
70 | |
71 - output for each column separately:: | |
72 | |
73 chr1 13326 13327 G 1 2 0 G/C 2 1,1 0,0 G 1 2 0 G 1 2 0 | |
74 chr1 13979 13980 T 1 2 0 T/C 2 1,1 0,0 T 1 2 0 T 1 2 0 | |
75 chr1 30922 30923 T 1 2 0 G 1 2 0 G 1 2 0 T 1 2 0 | |
76 etc. | |
77 | |
78 </help> | |
79 </tool> |