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