| Next changeset 1:a6c64723f5ce (2013-12-02) |
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README table_annovar.xml tool-data/annovar_index.loc tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 75b252cf390e README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Dec 02 15:29:39 2013 -0500 |
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| @@ -0,0 +1,24 @@ +ANNOVAR needs to be installed manually in the following way: + +1a) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of + the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) + +1b) If you do not have ANNOVAR installed, request annovar download and sign license here: + http://www.openbioinformatics.org/annovar/annovar_download_form.php + + i) Once downloaded, install annovar per the installation instructions and note the installation path. + + ii) Then download all desired databases for all desired builds as follows: + annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb> + + where <humandb> is location where all database files should be stored + and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool) + and <build> can be hg18 or hg19 for humans, also other organisms available. + + list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html + + iii) edit the tool-data/annovar.loc file to reflect location of humandb folder + +2) add the annovar scripts convert2annovar.pl and table_annovar.pl to your Galaxy user's path + +3) restart galaxy instance for changes in .loc file to take effect \ No newline at end of file |
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| diff -r 000000000000 -r 75b252cf390e table_annovar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/table_annovar.xml Mon Dec 02 15:29:39 2013 -0500 |
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| @@ -0,0 +1,85 @@ +<tool id="table_annovar" name="Annotate VCF" version="0.1"> + <description>with functional information using ANNOVAR</description> + + <requirements> + <requirement type="package">annovar</requirement> + </requirements> + + <command> + ## Convert VCF to AV input format. + convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput + + ## Variant annotation; make sure to include entry in indexes table for build database. + + #set protocol = [] + #set operation = [] + + ## Add gene annotations. + #if $gene_anns: + #silent protocol.append( str( $gene_anns ) ) + #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) ) + #end if + + ## Add regions. + #if $regions: + #silent protocol.append( str( $regions ) ) + #silent operation.append( ','.join( ['r' for t in range( str($regions).count(',') + 1 )] ) ) + #end if + + ## Add filters. + #if $filters: + #silent protocol.append( str( $filters ) ) + #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) ) + #end if + + #set protocol = ','.join( $protocol ) + #set operation = ','.join( $operation ) + + ## Reduce variants. + ; table_annovar.pl input.avinput ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring NA -buildver ${input.dbkey} --outfile output + + ## Copy annotated table to output. + ; cp output.${input.dbkey}_multianno.txt ${output} + </command> + + <inputs> + <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help=""> + <validator type="unspecified_build" /> + </param> + + <param name="gene_anns" type="select" multiple="True" optional="True" label="Gene Annotations" help="" > + <options from_data_table="annovar_indexes"> + <filter type="data_meta" key="dbkey" ref="input" column="1"/> + <filter type="static_value" name="type" value="gene_ann" column="2"/> + </options> + </param> + + <param name="regions" type="select" multiple="True" optional="True" label="Annotation Regions" help="" > + <options from_data_table="annovar_indexes"> + <filter type="data_meta" key="dbkey" ref="input" column="1"/> + <filter type="static_value" name="type" value="region" column="2"/> + </options> + </param> + + <param name="filters" type="select" multiple="True" label="Annotation Databases" help="" > + <options from_data_table="annovar_indexes"> + <filter type="data_meta" key="dbkey" ref="input" column="1"/> + <filter type="static_value" name="type" value="filter" column="2"/> + </options> + </param> + </inputs> + + <stdio> + <regex match=".*" source="both" level="log" description="tool progress"/> + </stdio> + + <outputs> + <data name="output" format="tabular"/> + </outputs> + + <tests> + </tests> + + <help> + </help> +</tool> |
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| diff -r 000000000000 -r 75b252cf390e tool-data/annovar_index.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/annovar_index.loc Mon Dec 02 15:29:39 2013 -0500 |
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| @@ -0,0 +1,20 @@ +# +# Database name (value), dbkey, type, and path. +# +# Sample entries for gene-based annotations: +#refGene hg19 gene_ann /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#wgEncodeGencodeCompV14 hg19 gene_ann /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +# +# Samples entries for region-based annotations: +# +#genomicSuperDups hg19 region /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#phastConsElements46way hg19 region /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +# +# Sample entries for filter-based annotations: +# +#1000g2012apr_all hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#avsift hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#snp137NonFlagged hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#esp6500si_all hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndice/ +#snp137 hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ +#cosmic64 hg19 filter /aut/bx/jgoecks/galaxy/data/Homo_sapiens/UCSC/hg19/AnnovarIndices/ \ No newline at end of file |
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| diff -r 000000000000 -r 75b252cf390e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Dec 02 15:29:39 2013 -0500 |
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| @@ -0,0 +1,7 @@ +<!-- ANNOVAR files --> +<tables> + <table name="annovar_indexes" comment_char="#"> + <columns>value, dbkey, type, path</columns> + <file path="tool-data/annovar_index.loc" /> + </table> +</tables> \ No newline at end of file |