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comparison vcf2pgSnp.xml @ 0:5fca46616675 draft default tip

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:55:29 -0400
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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>