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