# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1380895769 18000
# Node ID 6ad9205c1307f2e2caef91937ad00030dd2472d7
# Parent  bea875f081e8ada2df1da6bd5da873a1c4c329d5
Update to SnpEff version 3.3

diff -r bea875f081e8 -r 6ad9205c1307 README
--- a/README	Thu Jul 04 09:49:15 2013 -0500
+++ b/README	Fri Oct 04 09:09:29 2013 -0500
@@ -1,15 +1,18 @@
-These are galaxy tools for Snp Effect ( http://snpeff.sourceforge.net/ )
+These are galaxy tools for SnpEff ( http://snpeff.sourceforge.net/ )
+
+This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
+
+This will use the default location for genome reference downloads from the snpEff.config:
+data_dir = ~/snpEff/data/
+You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff.
+
 The genome reference options used by the tools:
     "SnpEff"  snpEff.xml
     "SnpEff Download" snpEff_download.xml
 are taken from: tool-data/snpeffect_genomedb.loc
 
-The tool-data/snpeffect_genomedb.loc.sample file has the genomes references from the SnpEffect dwnloads page:
-http://snpeff.sourceforge.net/download.html
-The values for snpeffect_genomedb.loc.sample were populated by:
-java -jar snpEff.jar cfg2table galaxy | grep 'option' | sed 's/^.*value="\([^"]*\)">\([^<]*\).*$/\1#\2/' | tr '#' '\t' >> snpeffect_genomedb.loc.sample
+There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
+  data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc 
+  data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc 
 
-This repository contains a tool_dependencies.xml file that will allow SnpEff and SnpSift to be automatically installed.   
-This will use the default location for genome reference downloads from the snpEff.config:
-data_dir = ~/snpEff/data/
 
diff -r bea875f081e8 -r 6ad9205c1307 data_manager/data_manager_snpEff_databases.py
--- a/data_manager/data_manager_snpEff_databases.py	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager/data_manager_snpEff_databases.py	Fri Oct 04 09:09:29 2013 -0500
@@ -46,7 +46,7 @@
                 genome_version = fields[0].strip()
                 if genome_version.startswith("Genome") or  genome_version.startswith("-"):
                     continue
-                description = fields[1].strip()
+                description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
         data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries   
     except Exception, e:
diff -r bea875f081e8 -r 6ad9205c1307 data_manager/data_manager_snpEff_databases.xml
--- a/data_manager/data_manager_snpEff_databases.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager/data_manager_snpEff_databases.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,10 +1,10 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.2" tool_type="manage_data">
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.3" tool_type="manage_data">
 	<description>Read the list of available snpEff databases</description>
 	<requirements>
-		<requirement type="package" version="3.2">snpEff</requirement>
+		<requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command interpreter="python">
-        data_manager_snpEff_databases.py --jar_path \$JAVA_JAR_PATH/snpEff.jar "$out_file"
+        data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
         </command>
 	<inputs>
 	</inputs>
diff -r bea875f081e8 -r 6ad9205c1307 data_manager/data_manager_snpEff_download.py
--- a/data_manager/data_manager_snpEff_download.py	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager/data_manager_snpEff_download.py	Fri Oct 04 09:09:29 2013 -0500
@@ -22,7 +22,7 @@
 # Download human database 'hg19'
 java -jar snpEff.jar download -v hg19
 
-        <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+        <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 
 snpEffectPredictor.bin
 regulation_HeLa-S3.bin
@@ -65,6 +65,8 @@
         sys.exit( return_code )
     ## search data_dir/genome_version for files
     regulation_pattern = 'regulation_(.+).bin'
+    #  annotation files that are included in snpEff by a flag
+    annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
     genome_path = os.path.join(data_dir,genome_version)
     if os.path.isdir(genome_path):
         for root, dirs, files in os.walk(genome_path):
@@ -78,8 +80,13 @@
                     m = re.match(regulation_pattern,fname)
                     if m:
                         name = m.groups()[0]
-                        data_table_entry = dict(value=genome_version, name=name)
+                        data_table_entry = dict(genome=genome_version,value=name, name=name)
                         _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
+                    elif fname in annotations_dict:
+                        value = annotations_dict[fname]
+                        name = value.lstrip('-')
+                        data_table_entry = dict(genome=genome_version,value=value, name=name)
+                        _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
     return data_manager_dict
 
 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
diff -r bea875f081e8 -r 6ad9205c1307 data_manager/data_manager_snpEff_download.xml
--- a/data_manager/data_manager_snpEff_download.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager/data_manager_snpEff_download.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,10 +1,10 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.2" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.3" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="3.2">snpEff</requirement>
+        <requirement type="package" version="3.3">snpEff</requirement>
     </requirements>
     <command interpreter="python">
-        data_manager_snpEff_download.py --jar_path \$JAVA_JAR_PATH/snpEff.jar --config \$JAVA_JAR_PATH/snpEff.config 
+        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
         --genome_version "${genome_databases.fields.value}"
         --organism "${genome_databases.fields.name}"
         "$out_file"
diff -r bea875f081e8 -r 6ad9205c1307 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager_conf.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -4,8 +4,7 @@
     <data_table name="snpeff_databases">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
-        </column>
+        <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
   </data_manager>
@@ -13,15 +12,28 @@
     <data_table name="snpeff_genomedb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="path" output_ref="out_file" >
+          <move type="directory" relativize_symlinks="True">
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/data</target>
+          </move>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/data</value_translation>
+          <value_translation type="function">abspath</value_translation>
         </column>
       </output>
     </data_table>
     <data_table name="snpeff_regulationdb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
-        </column>
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+    <data_table name="snpeff_annotations">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
   </data_manager>
diff -r bea875f081e8 -r 6ad9205c1307 snpEff.xml
--- a/snpEff.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpEff.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff" version="3.2">
+<tool id="snpEff" name="SnpEff" version="3.3">
 	<description>Variant effect and annotation</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
@@ -61,30 +61,34 @@
 
 	-->
 	<requirements>
-		<requirement type="package" version="3.2">snpEff</requirement>
+		<requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command>
-SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
+SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
-then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
+then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download  -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ;
 fi";
-java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
+java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
   -spliceSiteSize $spliceSiteSize
 #end if
 #if $filterIn and $filterIn.__str__ != 'no_filter':
-  -$filterIn 
+  $filterIn 
 #end if
 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
-  -$filterHomHet 
+  $filterHomHet 
 #end if
 #if $annotations and $annotations.__str__ != '':
-  -#slurp
-  #echo ' -'.join($annotations.__str__.split(','))
+  #echo ' '.join($annotations.__str__.split(','))
+#end if
+#if $extra_annotations and $extra_annotations.__str__ != '':
+  #echo ' '.join($extra_annotations.__str__.split(','))
+#end if
+#if $regulation and $regulation.__str__ != '':
+  -reg #echo ' -reg '.join($regulation.__str__.split(','))#
 #end if
 #if $filterOut and $filterOut.__str__ != '':
-  -#slurp
-  #echo ' -'.join($filterOut.__str__.split(','))
+  #echo ' '.join($filterOut.__str__.split(','))
 #end if
 #if str( $transcripts ) != 'None':
   -onlyTr $transcripts
@@ -96,7 +100,7 @@
   -stats $statsFile 
 #end if
 #if $offset.__str__ != '':
-  -${offset} 
+  ${offset} 
 #end if
 #if $chr.__str__.strip() != '':
   -chr "$chr" 
@@ -150,35 +154,43 @@
 
         	<param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
 			<option value="no_filter" selected="true">No filter (analyze everything)</option>
-			<option value="hom">Analyze homozygous sequence changes only </option>
-			<option value="het">Analyze heterozygous sequence changes only </option>
+			<option value="-hom">Analyze homozygous sequence changes only </option>
+			<option value="-het">Analyze heterozygous sequence changes only </option>
         	</param>
 
                 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
         	<param name="filterIn" type="select" display="radio" label="Filter sequence changes">
 			<option value="no_filter" selected="true">No filter (analyze everything)</option>
-			<option value="del">Analyze deletions only </option>
-			<option value="ins">Analyze insertions only </option>
-			<option value="mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
-			<option value="snp">Only SNPs (single nucleotide polymorphisms) </option>
+			<option value="-del">Analyze deletions only </option>
+			<option value="-ins">Analyze insertions only </option>
+			<option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
+			<option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
         	</param>
 
         	<param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
-			<option value="cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
-                        <option value="canon">Only use canonical transcripts.</option>
-                        <option value="geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
-                        <option value="hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
-                        <option value="lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
-                        <option value="oicr">Add OICR tag in VCF file. Default: false</option>
-                        <option value="onlyReg">Only use regulation tracks.</option>
-                        <option value="sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
+			<option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
+                        <option value="-canon">Only use canonical transcripts.</option>
+                        <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
+                        <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
+                        <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
+                        <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
+                        <option value="-onlyReg">Only use regulation tracks.</option>
+                        <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
+        	</param>
+
+        	<param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
+                       <help>These are available for only a few genomes</help>
+                       <!--GENOME	REG_NAME  -->
+                       <options from_data_table="snpeff_annotations">
+                               <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
+                       </options>
         	</param>
 
         	<param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
                        <help>These are available for only a few genomes</help>
                        <!--GENOME	REG_NAME  -->
-                       <options from_data_table="snpeffect_regulationdb">
-				<filter type="param_value" ref="genomeVersion" key="name" column="1" />
+                       <options from_data_table="snpeff_regulationdb">
+                               <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
                        </options>
         	</param>
 
@@ -186,21 +198,21 @@
         	<param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>
 
         	<param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
-			<option value="no-downstream">Do not show DOWNSTREAM changes </option>
-			<option value="no-intergenic">Do not show INTERGENIC changes </option>
-			<option value="no-intron">Do not show INTRON changes </option>
-			<option value="no-upstream">Do not show UPSTREAM changes </option>
-			<option value="no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
+			<option value="-no-downstream">Do not show DOWNSTREAM changes </option>
+			<option value="-no-intergenic">Do not show INTERGENIC changes </option>
+			<option value="-no-intron">Do not show INTRON changes </option>
+			<option value="-no-upstream">Do not show UPSTREAM changes </option>
+			<option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
         	</param>
 
         	<param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
 			<option value="" selected="true">Use default (based on input type)</option>
-			<option value="0">Force zero-based positions (both input and output)</option>
-			<option value="1">Force one-based positions (both input and output)</option>
+			<option value="-0">Force zero-based positions (both input and output)</option>
+			<option value="-1">Force one-based positions (both input and output)</option>
 		</param>
         	<param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.  You can prepend any string you want to the chromosome name.">
                                        <validator type="regex" message="No whitespace allows">^\S*$</validator>
- 
+
 		</param>
         	<param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
         	<param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
@@ -233,9 +245,7 @@
                 <param name="filterHomHet" value="no_filter"/>
                 <param name="filterIn" value="no_filter"/>
                 <param name="generate_stats" value="False"/>
-                <!--
-                <param name="filterOut" value="no-upstream"/>
-                -->
+                <param name="filterOut" value="+-no-upstream"/>
                 <output name="snpeff_output">
                     <assert_contents>
                         <!-- Check that an effect was added -->
@@ -258,7 +268,7 @@
                 <param name="outputFormat" value="vcf"/>
                 <param name="genomeVersion" value="testCase"/>
                 <param name="udLength" value="0"/>
-                <param name="filterHomHet" value="het"/>
+                <param name="filterHomHet" value="+-het"/>
                 <param name="filterIn" value="no_filter"/>
                 <!--
                 <param name="filterOut" value=""/>
@@ -300,7 +310,7 @@
                 <param name="udLength" value="0"/>
                 <param name="filterHomHet" value="no_filter"/>
                 <param name="filterIn" value="no_filter"/>
-                <param name="filterOut" value="no-upstream"/>
+                <param name="filterOut" value="+-no-upstream"/>
                 <param name="generate_stats" value="False"/>
                 <output name="snpeff_output">
                     <assert_contents>
diff -r bea875f081e8 -r 6ad9205c1307 snpSift_annotate.xml
--- a/snpSift_annotate.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpSift_annotate.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,14 +1,14 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2">
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.3">
 	<description>Annotate SNPs from dbSnp</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.2">snpEff</requirement>
+                <requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command>
-        java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd 
+        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
         #if $annotate.id :
           -id
         #elif $annotate.info_ids.__str__.strip() != '' :
diff -r bea875f081e8 -r 6ad9205c1307 snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpSift_caseControl.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,14 +1,14 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.2">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.3">
   <description>Count samples are in 'case' and 'control' groups.</description>
   <!-- 
     You will need to change the path to wherever your installation is.
     You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
   -->
   <requirements>
-                <requirement type="package" version="3.2">snpEff</requirement>
+                <requirement type="package" version="3.3">snpEff</requirement>
   </requirements>
   <command>
-    java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q 
+    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
     #if $name.__str__.strip() != '':
       -name $name
     #end if
diff -r bea875f081e8 -r 6ad9205c1307 snpSift_filter.xml
--- a/snpSift_filter.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpSift_filter.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,11 +1,11 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="3.2">
+<tool id="snpSift_filter" name="SnpSift Filter" version="3.3">
 	<options sanitize="False" />
 	<description>Filter variants using arbitrary expressions</description>
 	<requirements>
-                <requirement type="package" version="3.2">snpEff</requirement>
+                <requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
+		java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
                 #if $filterId and len($filterId.__str__.strip()) > 0:
 			--filterId = "$filterId"
                 #end if
diff -r bea875f081e8 -r 6ad9205c1307 snpSift_int.xml
--- a/snpSift_int.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpSift_int.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,14 +1,14 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="3.2">
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.3">
 	<description>Filter variants using intervals </description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.2">snpEff</requirement>
+                <requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+		java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
diff -r bea875f081e8 -r 6ad9205c1307 tool-data/snpeff_annotations.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff_annotations.loc.sample	Fri Oct 04 09:09:29 2013 -0500
@@ -0,0 +1,5 @@
+## Regulation Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+#genome	annotation_name description
+#GRCh37.71	nextprot	nextprot
+#GRCh37.71	motif	motif
diff -r bea875f081e8 -r 6ad9205c1307 tool-data/snpeff_regulationdb.loc.sample
--- a/tool-data/snpeff_regulationdb.loc.sample	Thu Jul 04 09:49:15 2013 -0500
+++ b/tool-data/snpeff_regulationdb.loc.sample	Fri Oct 04 09:09:29 2013 -0500
@@ -1,5 +1,4 @@
-## Databases for SnpEff 
+## Regulation Databases for SnpEff 
 ## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#Genome	Regulation_Name
-#GRCh37.70	CD4
+#genome	regulation_name description
+#GRCh37.70	CD4	CD4