--- a/snpEff.xml	Fri Aug 15 06:11:23 2014 -0400
+++ b/snpEff.xml	Tue Apr 07 10:54:12 2015 -0400
@@ -1,10 +1,11 @@
-<tool id="snpEff" name="SnpEff" version="3.6">
+<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
     <description>Variant effect and annotation</description>
     <expand macro="requirements" />
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <command>
+<![CDATA[
         java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 
         -c \$SNPEFF_JAR_PATH/snpEff.config 
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
@@ -34,7 +35,7 @@
         #if $statsFile:
           -stats $statsFile 
         #end if
-        #if $offset.__str__ != '':
+        #if $offset.__str__ != 'default':
           ${offset} 
         #end if
         #if $chr.__str__.strip() != '':
@@ -52,7 +53,7 @@
           #end if
           $snpDb.genomeVersion
         #elif $snpDb.genomeSrc == 'history':
-          -dataDir ${snpDb.snpeff_db.files_path}
+          -dataDir ${snpDb.snpeff_db.extra_files_path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
             #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
             #echo " "
@@ -76,8 +77,9 @@
         #end if
         #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
           ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
-          sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
+          sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
         #end if
+]]>
     </command>
     <inputs>
         <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
@@ -115,27 +117,33 @@
             <when value="cached">
                 <param name="genomeVersion" type="select" label="Genome">
                     <!--GENOME    DESCRIPTION-->
-                    <options from_data_table="snpeff_genomedb">
-                           <filter type="unique_value" column="0" />
+                    <options from_data_table="snpeffv_genomedb">
+                           <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
+                           <filter type="unique_value" column="2" />
                     </options>
                 </param>
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
                        <help>These are available for only a few genomes</help>
-                       <options from_data_table="snpeff_annotations">
-                           <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
-                           <filter type="unique_value" column="1" />
+                       <options from_data_table="snpeffv_annotations">
+                           <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
+                           <filter type="unique_value" column="3" />
                        </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>
-                       <options from_data_table="snpeff_regulationdb">
-                           <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
-                           <filter type="unique_value" column="1" />
+                       <options from_data_table="snpeffv_regulationdb">
+                           <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
+                           <filter type="unique_value" column="3" />
                        </options>
                 </param>
             </when>
             <when value="history">
-                <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
+                <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
+                    <options options_filter_attribute="metadata.snpeff_version" >
+                        <filter type="add_value" value="@SNPEFF_VERSION@" />
+                    </options>
+                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
+                </param>
                 <!-- From metadata -->
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
                     <help>These are available for only a few genomes</help>
@@ -151,7 +159,10 @@
                 </param>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
+                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+                    <help>@SNPEFF_DATABASE_URL@</help>
+                    <validator type="regex" message="A genome version name is required">\S+</validator>
+                </param>
             </when>
         </conditional>
 
@@ -184,6 +195,7 @@
             <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>
@@ -196,11 +208,12 @@
             <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
             <option value="-canon">Only use canonical transcripts</option>
             <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
-            <option value="-hgvs">Use HGVS annotations for amino acid sub-field</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</option>
             <option value="-onlyReg">Only use regulation tracks</option>
-            <option value="-sequenceOntolgy">Use Sequence Ontology terms</option>
+            <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
+            <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
+            <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
         </param>
         <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
         <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
@@ -213,7 +226,7 @@
         </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="default" 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>
         </param>
@@ -337,10 +350,13 @@
 
     </tests>
     <help>
+
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
 
 @EXTERNAL_DOCUMENTATION@
 
+@CITATION_SECTION@
+
     </help>
     <expand macro="citations" />
 </tool>