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planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:58:50 -0500
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1 <tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.2">
2 <description>with functional information using ANNOVAR</description>
3
4 <requirements>
5 <requirement type="package">annovar</requirement>
6 <requirement type="set_environment">SCRIPT_PATH</requirement>
7 </requirements>
8
9 <command>
10 ## Convert VCF to AV input format.
11 #if str($out_format) == "tabular":
12 convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput ;
13 #set tab_anno_input = "input.avinput"
14 #else:
15 #set tab_anno_input = $input
16 #end if
17
18 ## Variant annotation; make sure to include entry in indexes table for build database.
19
20 #set protocol = []
21 #set operation = []
22
23 ## Add gene annotations.
24 #if $gene_anns:
25 #silent protocol.append( str( $gene_anns ) )
26 #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) )
27 #end if
28
29 ## Add regions.
30 #if $regions:
31 #silent protocol.append( str( $regions ) )
32 #silent operation.append( ','.join( ['r' for t in range( str($regions).count(',') + 1 )] ) )
33 #end if
34
35 ## Add filters.
36 #if $filters:
37 #silent protocol.append( str( $filters ) )
38 #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) )
39 #end if
40
41 #set protocol = ','.join( $protocol )
42 #set operation = ','.join( $operation )
43
44 ## Annotate variants.
45 table_annovar.pl ${tab_anno_input} ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring '.' -buildver ${input.dbkey} --outfile output
46
47 ## Add option to consume/produce VCF.
48 #if str($out_format) == "vcf":
49 --vcfinput
50 #end if
51
52 ## Post-processing: process annotated table to remove "NA" strings from numerical columns if
53 ## tabular. Copy to output.
54 #if str($out_format) == "tabular":
55 ; cat output.${input.dbkey}_multianno.txt | python \${SCRIPT_PATH}/replace_NA.py > ${output}
56 #else:
57 ; cp output.${input.dbkey}_multianno.vcf ${output}
58 #end if
59 </command>
60
61 <inputs>
62 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
63 <validator type="unspecified_build" />
64 </param>
65
66 <param name="gene_anns" type="select" multiple="True" optional="True" label="Gene Annotations" help="" >
67 <options from_data_table="annovar_indexes">
68 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
69 <filter type="static_value" name="type" value="gene_ann" column="2"/>
70 </options>
71 </param>
72
73 <param name="regions" type="select" multiple="True" optional="True" label="Annotation Regions" help="" >
74 <options from_data_table="annovar_indexes">
75 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
76 <filter type="static_value" name="type" value="region" column="2"/>
77 </options>
78 </param>
79
80 <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" >
81 <options from_data_table="annovar_indexes">
82 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
83 <filter type="static_value" name="type" value="filter" column="2"/>
84 </options>
85 </param>
86
87 <param name="out_format" type="select" label="Output data type">
88 <option value="vcf">VCF</option>
89 <option value="tabular">Tabular</option>
90 </param>
91
92 </inputs>
93
94 <stdio>
95 <regex match=".*" source="both" level="log" description="tool progress"/>
96 </stdio>
97
98 <outputs>
99 <data name="output" format="tabular">
100 <change_format>
101 <when input="out_format" value="vcf" format="vcf"/>
102 </change_format>
103 </data>
104 </outputs>
105
106 <tests>
107 </tests>
108
109 <help>
110 **What it does**
111
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
113 VCF dataset or a VCF dataset with the annotations in INFO fields.
114
115 **ANNOVAR Website and Documentation**
116
117 Website: http://www.openbioinformatics.org/annovar/
118
119 Paper: http://nar.oxfordjournals.org/content/38/16/e164
120
121 **Important Usage Note**
122
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
124
125 </help>
126 </tool>