diff snpSift_caseControl.xml @ 8:2f40467536cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

--- a/snpSift_caseControl.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_caseControl.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,16 +10,16 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
-    #if $name.__str__.strip() != '':
-      -name $name
+    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
+    #if str($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>
@@ -118,8 +118,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
-@CITATION_SECTION@
-
 ]]>
-  </help>
+    </help>
+    <expand macro="citations" />
 </tool>