--- a/snpEff.xml	Thu Jun 26 08:40:30 2014 -0500
+++ b/snpEff.xml	Mon Oct 20 08:37:01 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff" version="3.6">
+<tool id="snpEff" name="SnpEff" version="4.0.0">
     <description>Variant effect and annotation</description>
     <expand macro="requirements" />
     <macros>
@@ -40,7 +40,7 @@
         #if $chr.__str__.strip() != '':
           -chr "$chr" 
         #end if
-          $noLog 
+        $noLog 
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
@@ -176,11 +176,12 @@
             <option value="-cancer">Perform 'cancer' comparissons (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 Ontolgy 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."/>