Mercurial > repos > miller-lab > snp_analysis_conversion

comparison snp_analysis_conversion/vcf2pgSnp.xml @ 0:3871157bc013

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Initial upload to toolshed.g2 via UI.
author cathy
date Tue, 28 May 2013 17:01:14 -0400
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1 <tool id="vcf2pgSnp" name="VCF to pgSnp" version="1.0.0" hidden="false">
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
36 **Dataset formats**
37
38 The input dataset is in VCF_ format.
39 The output dataset is pgSnp_. (`Dataset missing?`_)
40
41 .. _VCF: ./static/formatHelp.html#vcf
42 .. _pgSnp: ./static/formatHelp.html#pgSnp
43 .. _Dataset missing?: ./static/formatHelp.html
44
45 -----
46
47 **What it does**
48
49 This converts a VCF dataset to pgSnp format, using chromosome counts for
50 the allele frequencies. If there is more than one column (individual)
51 of SNP data, it can either combine all columns as a population, or just
52 convert a single selected column.
53
54 -----
55
56 **Examples**
57
58 - input::
59
60 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
61 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
62 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
63 etc.
64
65 - output as a population::
66
67 chr1 13326 13327 G/C 2 7,1 0,0
68 chr1 13979 13980 T/C 2 7,1 0,0
69 chr1 30922 30923 G/T 2 4,4 0,0
70 etc.
71
72 - output for column 10::
73
74 chr1 13326 13327 G 1 2 0
75 chr1 13979 13980 T 1 2 0
76 chr1 30922 30923 T 1 2 0
77 etc.
78
79 </help>
80 </tool>