Mercurial > repos > jjohnson > snpsift

diff snpSift_extractFields.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 824f78c0d0df
children
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--- a/snpSift_extractFields.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_extractFields.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,9 +10,9 @@
     <command><![CDATA[
         cat "$input"
         #if $one_effect_per_line:
-          | \$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl
+          | "\$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl"
         #end if 
-        | java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar extractFields 
+        | java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" extractFields 
         #if $separator:
           -s '$separator'  
         #end if
@@ -21,7 +21,7 @@
         #end if
         -
         #echo ' '.join(['"%s"' % x for x in $extract.split()])
-        > $output
+        > "$output"
 ]]>
     </command>
     <inputs>
@@ -214,8 +214,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#Extract
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>