diff snpSift_annotate.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_annotate.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_annotate.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,13 +10,13 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
         #if $annotate.id :
           -id
-        #elif $annotate.info_ids.__str__.strip() != '' :
+        #elif str($annotate.info_ids).strip() != '' :
           -info "$annotate.info_ids"
         #end if          
-        -q $dbSnp $input > $output 
+        -q "$dbSnp" "$input" > "$output" 
 ]]>
     </command>
     <inputs>
@@ -94,10 +94,8 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#annotate
 
-@CITATION_SECTION@
-
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>