--- a/snpSift_int.xml	Thu Oct 23 06:06:25 2014 -0500
+++ b/snpSift_int.xml	Wed Dec 09 14:03:26 2015 -0500
@@ -1,14 +1,17 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
+<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
     <description>Filter variants using intervals</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
+    <macros>
+        <import>snpSift_macros.xml</import>
+    </macros>
     <expand macro="requirements" />
-    <macros>
-        <import>snpEff_macros.xml</import>
-    </macros>
-    <command>
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
         java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -19,7 +22,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="annotate_5.vcf"/>
@@ -44,14 +46,15 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 You can filter using intervals (BED file).
 
 @EXTERNAL_DOCUMENTATION@
-	http://snpeff.sourceforge.net/SnpSift.html#intervals
+    http://snpeff.sourceforge.net/SnpSift.html#intervals
 
 @CITATION_SECTION@
 
+]]>
     </help>
 </tool>