Mercurial > repos > yhoogstrate > featurecounts_valid_gff

changeset 25:7d51c3e8e230

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Uploaded
author yhoogstrate
date Thu, 09 Jan 2014 04:54:59 -0500
parents 833116c366f5
children 94d20952a7cb
files featureCounts.xml
diffstat 1 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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>