diff snpSift_caseControl.xml @ 4:baf6602903e1

Uploaded

--- a/snpSift_caseControl.xml	Thu Oct 23 06:06:25 2014 -0500
+++ b/snpSift_caseControl.xml	Wed Dec 09 14:03:26 2015 -0500
@@ -1,13 +1,15 @@
-<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>
+        <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 -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
     #if $name.__str__.strip() != '':
       -name $name
@@ -18,6 +20,7 @@
       -tfam "$ctrl.tfam"
     #end if
     $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**
 
@@ -118,5 +120,6 @@
 
 @CITATION_SECTION@
 
+]]>
   </help>
 </tool>