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comparison table_annovar.xml @ 0:75b252cf390e

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author devteam
date Mon, 02 Dec 2013 15:29:39 -0500
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1 <tool id="table_annovar" name="Annotate VCF" version="0.1">
2 <description>with functional information using ANNOVAR</description>
3
4 <requirements>
5 <requirement type="package">annovar</requirement>
6 </requirements>
7
8 <command>
9 ## Convert VCF to AV input format.
10 convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput
11
12 ## Variant annotation; make sure to include entry in indexes table for build database.
13
14 #set protocol = []
15 #set operation = []
16
17 ## Add gene annotations.
18 #if $gene_anns:
19 #silent protocol.append( str( $gene_anns ) )
20 #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) )
21 #end if
22
23 ## Add regions.
24 #if $regions:
25 #silent protocol.append( str( $regions ) )
26 #silent operation.append( ','.join( ['r' for t in range( str($regions).count(',') + 1 )] ) )
27 #end if
28
29 ## Add filters.
30 #if $filters:
31 #silent protocol.append( str( $filters ) )
32 #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) )
33 #end if
34
35 #set protocol = ','.join( $protocol )
36 #set operation = ','.join( $operation )
37
38 ## Reduce variants.
39 ; table_annovar.pl input.avinput ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring NA -buildver ${input.dbkey} --outfile output
40
41 ## Copy annotated table to output.
42 ; cp output.${input.dbkey}_multianno.txt ${output}
43 </command>
44
45 <inputs>
46 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
47 <validator type="unspecified_build" />
48 </param>
49
50 <param name="gene_anns" type="select" multiple="True" optional="True" label="Gene Annotations" help="" >
51 <options from_data_table="annovar_indexes">
52 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
53 <filter type="static_value" name="type" value="gene_ann" column="2"/>
54 </options>
55 </param>
56
57 <param name="regions" type="select" multiple="True" optional="True" label="Annotation Regions" help="" >
58 <options from_data_table="annovar_indexes">
59 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
60 <filter type="static_value" name="type" value="region" column="2"/>
61 </options>
62 </param>
63
64 <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" >
65 <options from_data_table="annovar_indexes">
66 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
67 <filter type="static_value" name="type" value="filter" column="2"/>
68 </options>
69 </param>
70 </inputs>
71
72 <stdio>
73 <regex match=".*" source="both" level="log" description="tool progress"/>
74 </stdio>
75
76 <outputs>
77 <data name="output" format="tabular"/>
78 </outputs>
79
80 <tests>
81 </tests>
82
83 <help>
84 </help>
85 </tool>