Mercurial > repos > jjohnson > snpsift

diff snpSift_vcfCheck.xml @ 8:2f40467536cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:53:30 -0400
parents baf6602903e1
children
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--- a/snpSift_vcfCheck.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_vcfCheck.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
+      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -35,8 +35,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>