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comparison tools/maf/vcf_to_maf_customtrack.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track">
2 <description>for display at UCSC</description>
3 <command interpreter="python">vcf_to_maf_customtrack.py '$out_file1'
4 #if $vcf_source_type.vcf_file
5 '${vcf_source_type.vcf_file[0].vcf_input.dbkey}'
6 #else
7 '?'
8 #end if
9 ${vcf_source_type.vcf_source} -n '$track_name'
10 #for $vcf_repeat in $vcf_source_type.vcf_file
11 '${vcf_repeat.vcf_input}'
12 #if $vcf_source_type.vcf_source == '-p'
13 '${vcf_repeat.population_name}'
14 #end if
15 #end for
16 -g
17 </command>
18 <inputs>
19 <param name="track_name" type="text" label="Custom Track Name" value="Galaxy Custom Track" size="30" />
20 <conditional name="vcf_source_type">
21 <param name="vcf_source" type="select" label="VCF Source Source Type">
22 <option value="-p" selected="true">Per Population (file)</option>
23 <option value="-s">Per Sample</option>
24 </param>
25 <when value="-p">
26 <repeat name="vcf_file" title="VCF population file" min="1">
27 <param format="tabular" name="vcf_input" type="data" label="VCF file"/>
28 <param name="population_name" type="text" label="Name for this population" value=""/>
29 </repeat>
30 </when>
31 <when value="-s">
32 <repeat name="vcf_file" title="VCF sample file" min="1">
33 <param format="tabular" name="vcf_input" type="data" label="VCF file"/>
34 <!-- add column count validator >= 8? -->
35 </repeat>
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data format="mafcustomtrack" name="out_file1" />
41 </outputs>
42 <!-- <tests>
43 <test>
44 <param name="track_name" value="Galaxy Custom Track"/>
45 <param name="vcf_source" value="Per Population"/>
46 <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/>
47 <param name="population_name" value=""/>
48 <output name="out_file1" file="vcf_to_maf_population_out.mafcustomtrack"/>
49 </test>
50 <test>
51 <param name="track_name" value="Galaxy Custom Track"/>
52 <param name="vcf_source" value="Per Sample"/>
53 <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/>
54 <output name="out_file1" file="vcf_to_maf_sample_out.mafcustomtrack"/>
55 </test>
56 </tests> -->
57 <help>
58 **What it does**
59
60 This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.
61
62 This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.
63
64 *Unknown nucleotides* are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.
65
66 **Example**
67
68 Starting with a VCF::
69
70 ##fileformat=VCFv3.3
71 ##fileDate=20090805
72 ##source=myImputationProgramV3.1
73 ##reference=1000GenomesPilot-NCBI36
74 ##phasing=partial
75 ##INFO=NS,1,Integer,"Number of Samples With Data"
76 ##INFO=DP,1,Integer,"Total Depth"
77 ##INFO=AF,-1,Float,"Allele Frequency"
78 ##INFO=AA,1,String,"Ancestral Allele"
79 ##INFO=DB,0,Flag,"dbSNP membership, build 129"
80 ##INFO=H2,0,Flag,"HapMap2 membership"
81 ##FILTER=q10,"Quality below 10"
82 ##FILTER=s50,"Less than 50% of samples have data"
83 ##FORMAT=GT,1,String,"Genotype"
84 ##FORMAT=GQ,1,Integer,"Genotype Quality"
85 ##FORMAT=DP,1,Integer,"Read Depth"
86 ##FORMAT=HQ,2,Integer,"Haplotype Quality"
87 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
88 20 14370 rs6054257 G A 29 0 NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:-1,-1
89 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:-1,-1
90 20 1110696 rs6040355 A G,T 67 0 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:-1,-1
91 20 1230237 . T . 47 0 NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2:-1,-1
92 20 1234567 microsat1 G D4,IGA 50 0 NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
93
94
95
96
97 Under the following conditions: **VCF Source type:** *Per Population (file)*, **Name for this population:** *CHB+JPT*
98 Results in the following MAF custom track::
99
100 track name="Galaxy Custom Track" visibility=pack
101 ##maf version=1
102 a score=0
103 s hg18.chr20 14369 1 + 14370 G
104 s CHB+JPT_1.1 0 1 + 1 A
105
106 a score=0
107 s hg18.chr20 17329 1 + 17330 T
108 s CHB+JPT_1.2 0 1 + 1 A
109
110 a score=0
111 s hg18.chr20 1110695 1 + 1110696 A
112 s CHB+JPT_1.3 0 1 + 1 G
113 s CHB+JPT_2.3 0 1 + 1 T
114
115 a score=0
116 s hg18.chr20 1230236 1 + 1230237 T
117 s CHB+JPT_1.4 0 1 + 1 .
118
119 a score=0
120 s hg18.chr20 1234565 5 + 1234572 *G--***
121 s CHB+JPT_1.5 0 1 + 1 *------
122 s CHB+JPT_2.5 0 7 + 7 *GGA***
123
124
125 </help>
126 </tool>
127