--- a/snpEff.xml	Fri Feb 19 08:26:25 2016 -0500
+++ b/snpEff.xml	Tue Jun 07 10:03:17 2016 -0400
@@ -1,11 +1,11 @@
 <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>
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
 <![CDATA[
         java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
@@ -14,6 +14,17 @@
         #if $spliceSiteSize and str($spliceSiteSize) != '':
           -spliceSiteSize "$spliceSiteSize"
         #end if
+        #if $spliceRegion.setSpliceRegions == 'yes':
+          #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
+            -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
+          #end if
+          #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
+            -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
+          #end if
+          #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
+            -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
+          #end if
+        #end if
         #if $annotations and str($annotations) != '':
           #echo " "
           #echo ' '.join(str($annotations).split(','))
@@ -87,8 +98,6 @@
 
         <param name="inputFormat" type="select" label="Input format">
             <option value="vcf" selected="true">VCF</option>
-            <option value="txt">Tabular (Deprecated)</option>
-            <option value="pileup">Pileup (Deprecated)</option>
             <option value="bed">BED (Deprecated)</option>
         </param>
 
@@ -96,7 +105,6 @@
             <param name="outputFormat" type="select" label="Output format">
                 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
                 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
-                <option value="txt">Tabular</option>
                 <option value="bed">BED</option>
                 <option value="bedAnn">BED annotations</option>
             </param>
@@ -104,7 +112,6 @@
             <when value="gatk">
                 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
             </when>
-            <when value="txt" />
             <when value="bed" />
             <when value="bedAnn" />
         </conditional>
@@ -190,6 +197,19 @@
             <option value="9">9 bases</option>
         </param>
 
+        <conditional name="spliceRegion">
+            <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
+                <option value="no">Use Defaults</option>
+                <option value="yes">Set Splice Region Parameters</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
+                <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/>
+                <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/>
+            </when>
+        </conditional>
+
         <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
             <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
             <option value="-canon">Only use canonical transcripts</option>
@@ -200,7 +220,13 @@
             <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>
+            <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
+	    <option value="-noHgvs">Do not add HGVS annotations.</option>
+	    <option value="-noLof">Do not add LOF and NMD annotations.</option>
+	    <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
+	    <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
         </param>
+        <!-- -cancerSamples <file>           : Two column TXT file defining 'oringinal \t derived' samples. -->
         <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."/>
         <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
@@ -278,12 +304,11 @@
             <validator type="regex" message="No whitespace allowed">^\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"/>
+        <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
     </inputs>
     <outputs>
         <data format="vcf" name="snpeff_output" >
             <change_format>
-                <when input="outputConditional.outputFormat" value="txt" format="tabular" />
                 <when input="outputConditional.outputFormat" value="bed" format="bed" />
                 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
             </change_format>
@@ -301,7 +326,7 @@
             <has_text text="SnpEff: Variant analysis" />
             </assert_contents>
         </output>
-        --> 
+        -->
         <!-- Setting filterOut throws exception in twilltestcase.py
         <test>
         <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
@@ -318,7 +343,7 @@
             </assert_contents>
         </output>
         </test>
-        --> 
+        -->
 
         <test>
         <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
@@ -361,14 +386,13 @@
         -->
 
     </tests>
-    <help>
+    <help><![CDATA[
 
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
 
 @EXTERNAL_DOCUMENTATION@
 
-@CITATION_SECTION@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>