# HG changeset patch
# User devteam
# Date 1386016179 18000
# Node ID 75b252cf390e723a489767da7fb5fa6af367299f

Uploaded

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
@@ -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
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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
@@ -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>
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
@@ -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/
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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
@@ -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>
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