# HG changeset patch
# User yhoogstrate
# Date 1389261299 18000
# Node ID 7d51c3e8e2307a6807c1d7c14be925c47698fca2
# Parent  833116c366f5fe504807a72c22f538f3f06fc865
Uploaded

diff -r 833116c366f5 -r 7d51c3e8e230 featureCounts.xml
--- a/featureCounts.xml	Thu Jan 09 02:57:10 2014 -0500
+++ b/featureCounts.xml	Thu Jan 09 04:54:59 2014 -0500
@@ -38,20 +38,21 @@
 				${alignment.file}
 			#end for
 			
-			> /dev/null 2> /dev/null
-		
+			2>&1
 		
-		#if $format == "complex" or $format.value == "complex"
-			; mv tmp.txt $output
+		<!-- #if $format == "complex" or $format.value == "complex" -->
+		<!-- ; mv tmp.txt $output -->
 		#elif $format == "tabdel_default" or $format.value == "tabdel_default"
+			; cp $output tmp.txt
 			; egrep -v "^#" tmp.txt > tmp2.txt
 			; cut -f 1,7 tmp2.txt > tmp_left.txt
 			; cut -f 6 tmp2.txt > tmp_right.txt
 			; paste tmp_left.txt tmp_right.txt > $output
-			; rm tmp.txt tmp2.txt tmp_left.txt tmp_right.txt
+			<!-- ; rm tmp.txt tmp2.txt tmp_left.txt tmp_right.txt -->
 		#elif $format == "tabdel_short" or $format.value == "tabdel_short"
+			; cp $output tmp.txt
 			; egrep -v "^#" tmp.txt | cut -f 1,7 > $output
-			; rm tmp.txt
+			<!-- ; rm tmp.txt -->
 		#end if
 	</command>