--- a/snpSift_caseControl.xml	Tue Oct 13 17:31:24 2015 -0400
+++ b/snpSift_caseControl.xml	Tue Jun 07 09:41:13 2016 -0400
@@ -1,6 +1,6 @@
-<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)
     -->
     <macros>
@@ -8,17 +8,19 @@
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
-    #if $name.__str__.strip() != '':
-      -name $name
+    <expand macro="version_command" />
+    <command><![CDATA[
+    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
+    #if str($name).strip() != '':
+      -name "$name"
     #end if
     #if $ctrl.ctrl_src == 'caseString':
-      '$ctrl.caseControlStr'
+      '$ctrl.caseControlStr' 
     #else
       -tfam "$ctrl.tfam"
     #end if
-    $input > $output
+    "$input" > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -28,7 +30,7 @@
             <option value="tfam">TFAM file</option>
         </param>
         <when value="caseString">
-            <param name="caseControlStr" type="text" label="Case / Control column designation">
+            <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
             <help>
                 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
             </help>
@@ -84,17 +86,17 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 **SnpSift CaseControl**
 
-Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
+Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 
 
-Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
+Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 
 
 This command adds two annotations to the VCF file:
 
- - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
+ - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 
 
   "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
 
@@ -108,7 +110,7 @@
 
   - Hom/Het case = "hom"
 
-  - Hom/Het control = "any"
+  - Hom/Het control = "any"  
 
   - Case / Control column designation = ""++++------"
 
@@ -116,7 +118,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
-@CITATION_SECTION@
-
-  </help>
+]]>
+    </help>
+    <expand macro="citations" />
 </tool>