--- a/snpSift_caseControl.xml	Thu Jan 22 08:39:07 2015 -0500
+++ b/snpSift_caseControl.xml	Tue Jun 07 10:04:09 2016 -0400
@@ -1,23 +1,26 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0">
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0">
     <description>Count samples are in 'case' and 'control' groups.</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
-    <command>
-    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
-    #if $name.__str__.strip() != '':
-      -name $name
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
+    #if str($name).strip() != '':
+      -name "$name"
     #end if
     #if $ctrl.ctrl_src == 'caseString':
       '$ctrl.caseControlStr' 
     #else
       -tfam "$ctrl.tfam"
     #end if
-    $input > $output
+    "$input" > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -45,7 +48,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="test.private.01.vcf"/>
@@ -84,7 +86,7 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 **SnpSift CaseControl**
 
@@ -116,7 +118,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
-@CITATION_SECTION@
-
-  </help>
+]]>
+    </help>
+    <expand macro="citations" />
 </tool>