Mercurial > repos > devteam > table_annovar
comparison table_annovar.xml @ 7:08b003ee9db7 draft
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author | devteam |
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date | Wed, 22 Apr 2015 23:52:01 -0400 |
parents | 091154194ce8 |
children | d4e292ddda05 |
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6:091154194ce8 | 7:08b003ee9db7 |
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1 <tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.1"> | 1 <tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.2"> |
2 <description>with functional information using ANNOVAR</description> | 2 <description>with functional information using ANNOVAR</description> |
3 | 3 |
4 <requirements> | 4 <requirements> |
5 <requirement type="package">annovar</requirement> | 5 <requirement type="package">annovar</requirement> |
6 <requirement type="set_environment">SCRIPT_PATH</requirement> | 6 <requirement type="set_environment">SCRIPT_PATH</requirement> |
7 </requirements> | 7 </requirements> |
8 | 8 |
9 <command> | 9 <command> |
10 ## Convert VCF to AV input format. | 10 ## Convert VCF to AV input format. |
11 convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput | 11 #if str($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 | |
12 | 17 |
13 ## Variant annotation; make sure to include entry in indexes table for build database. | 18 ## Variant annotation; make sure to include entry in indexes table for build database. |
14 | 19 |
15 #set protocol = [] | 20 #set protocol = [] |
16 #set operation = [] | 21 #set operation = [] |
17 | 22 |
18 ## Add gene annotations. | 23 ## Add gene annotations. |
32 #silent protocol.append( str( $filters ) ) | 37 #silent protocol.append( str( $filters ) ) |
33 #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) ) | 38 #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) ) |
34 #end if | 39 #end if |
35 | 40 |
36 #set protocol = ','.join( $protocol ) | 41 #set protocol = ','.join( $protocol ) |
37 #set operation = ','.join( $operation ) | 42 #set operation = ','.join( $operation ) |
38 | 43 |
39 ## Reduce variants. | 44 ## Annotate variants. |
40 ; 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 | 45 table_annovar.pl ${tab_anno_input} ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring '.' -buildver ${input.dbkey} --outfile output |
41 | 46 |
42 ## Process annotated table to remove "NA" strings from numerical columns and copy to output. | 47 ## Add option to consume/produce VCF. |
43 ; cat output.${input.dbkey}_multianno.txt | python \$SCRIPT_PATH/replace_NA.py > ${output} | 48 #if str($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 | |
44 </command> | 59 </command> |
45 | 60 |
46 <inputs> | 61 <inputs> |
47 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help=""> | 62 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help=""> |
48 <validator type="unspecified_build" /> | 63 <validator type="unspecified_build" /> |
59 <options from_data_table="annovar_indexes"> | 74 <options from_data_table="annovar_indexes"> |
60 <filter type="data_meta" key="dbkey" ref="input" column="1"/> | 75 <filter type="data_meta" key="dbkey" ref="input" column="1"/> |
61 <filter type="static_value" name="type" value="region" column="2"/> | 76 <filter type="static_value" name="type" value="region" column="2"/> |
62 </options> | 77 </options> |
63 </param> | 78 </param> |
64 | 79 |
65 <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" > | 80 <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" > |
66 <options from_data_table="annovar_indexes"> | 81 <options from_data_table="annovar_indexes"> |
67 <filter type="data_meta" key="dbkey" ref="input" column="1"/> | 82 <filter type="data_meta" key="dbkey" ref="input" column="1"/> |
68 <filter type="static_value" name="type" value="filter" column="2"/> | 83 <filter type="static_value" name="type" value="filter" column="2"/> |
69 </options> | 84 </options> |
70 </param> | 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 | |
71 </inputs> | 92 </inputs> |
72 | 93 |
73 <stdio> | 94 <stdio> |
74 <regex match=".*" source="both" level="log" description="tool progress"/> | 95 <regex match=".*" source="both" level="log" description="tool progress"/> |
75 </stdio> | 96 </stdio> |
76 | 97 |
77 <outputs> | 98 <outputs> |
78 <data name="output" format="tabular"/> | 99 <data name="output" format="tabular"> |
100 <change_format> | |
101 <when input="out_format" value="vcf" format="vcf"/> | |
102 </change_format> | |
103 </data> | |
79 </outputs> | 104 </outputs> |
80 | 105 |
81 <tests> | 106 <tests> |
82 </tests> | 107 </tests> |
83 | 108 |
84 <help> | 109 <help> |
85 **What it does** | 110 **What it does** |
86 | 111 |
87 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 | 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 |
88 VCF dataset. | 113 VCF dataset or a VCF dataset with the annotations in INFO fields. |
89 | 114 |
90 **ANNOVAR Website and Documentation** | 115 **ANNOVAR Website and Documentation** |
91 | 116 |
92 Website: http://www.openbioinformatics.org/annovar/ | 117 Website: http://www.openbioinformatics.org/annovar/ |
93 | 118 |