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1 <tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.2">
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2 <description>with functional information using ANNOVAR</description>
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3
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4 <requirements>
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5 <requirement type="package">annovar</requirement>
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6 <requirement type="set_environment">SCRIPT_PATH</requirement>
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7 </requirements>
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8
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9 <command>
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10 ## Convert VCF to AV input format.
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11 #if str($out_format) == "tabular":
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12 convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput ;
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13 #set tab_anno_input = "input.avinput"
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14 #else:
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15 #set tab_anno_input = $input
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16 #end if
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17
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18 ## Variant annotation; make sure to include entry in indexes table for build database.
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19
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20 #set protocol = []
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21 #set operation = []
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22
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23 ## Add gene annotations.
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24 #if $gene_anns:
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25 #silent protocol.append( str( $gene_anns ) )
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26 #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) )
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27 #end if
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28
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29 ## Add regions.
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30 #if $regions:
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31 #silent protocol.append( str( $regions ) )
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32 #silent operation.append( ','.join( ['r' for t in range( str($regions).count(',') + 1 )] ) )
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33 #end if
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34
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35 ## Add filters.
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36 #if $filters:
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37 #silent protocol.append( str( $filters ) )
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38 #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) )
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39 #end if
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40
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41 #set protocol = ','.join( $protocol )
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42 #set operation = ','.join( $operation )
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43
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44 ## Annotate variants.
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45 table_annovar.pl ${tab_anno_input} ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring '.' -buildver ${input.dbkey} --outfile output
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46
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47 ## Add option to consume/produce VCF.
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48 #if str($out_format) == "vcf":
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49 --vcfinput
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50 #end if
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51
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52 ## Post-processing: process annotated table to remove "NA" strings from numerical columns if
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53 ## tabular. Copy to output.
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54 #if str($out_format) == "tabular":
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55 ; cat output.${input.dbkey}_multianno.txt | python \${SCRIPT_PATH}/replace_NA.py > ${output}
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56 #else:
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57 ; cp output.${input.dbkey}_multianno.vcf ${output}
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58 #end if
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59 </command>
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60
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61 <inputs>
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62 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
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63 <validator type="unspecified_build" />
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64 </param>
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65
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66 <param name="gene_anns" type="select" multiple="True" optional="True" label="Gene Annotations" help="" >
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67 <options from_data_table="annovar_indexes">
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68 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
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69 <filter type="static_value" name="type" value="gene_ann" column="2"/>
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70 </options>
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71 </param>
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72
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73 <param name="regions" type="select" multiple="True" optional="True" label="Annotation Regions" help="" >
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74 <options from_data_table="annovar_indexes">
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75 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
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76 <filter type="static_value" name="type" value="region" column="2"/>
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77 </options>
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78 </param>
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79
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80 <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" >
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81 <options from_data_table="annovar_indexes">
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82 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
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83 <filter type="static_value" name="type" value="filter" column="2"/>
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84 </options>
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85 </param>
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86
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87 <param name="out_format" type="select" label="Output data type">
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88 <option value="vcf">VCF</option>
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89 <option value="tabular">Tabular</option>
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90 </param>
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91
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92 </inputs>
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93
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94 <stdio>
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95 <regex match=".*" source="both" level="log" description="tool progress"/>
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96 </stdio>
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97
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98 <outputs>
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99 <data name="output" format="tabular">
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100 <change_format>
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101 <when input="out_format" value="vcf" format="vcf"/>
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102 </change_format>
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103 </data>
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104 </outputs>
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105
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106 <tests>
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107 </tests>
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108
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109 <help>
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110 **What it does**
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111
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112 This tool will annotate variants using specified gene annotations, regions, and filtering databases. Input is a VCF dataset, and output is a table of annotations for each variant in the
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113 VCF dataset or a VCF dataset with the annotations in INFO fields.
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114
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115 **ANNOVAR Website and Documentation**
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116
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117 Website: http://www.openbioinformatics.org/annovar/
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118
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119 Paper: http://nar.oxfordjournals.org/content/38/16/e164
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120
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121 **Important Usage Note**
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122
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123 ANNOVAR is open-source and free for non-profit use. If you use it for commercial purposes, please contact BIOBASE (info@biobase-international.com) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license
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124
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125 </help>
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126 </tool>
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