Mercurial > repos > bgruening > deeptools

diff bamCorrelate.xml @ 3:9441b4e5d2d6 draft

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Uploaded
author bgruening
date Sat, 16 Nov 2013 07:50:32 -0500
parents a22ccc261bb3
children c54d31467be4
line wrap: on
line diff
--- a/bamCorrelate.xml	Fri Nov 15 11:02:32 2013 -0500
+++ b/bamCorrelate.xml	Sat Nov 16 07:50:32 2013 -0500
@@ -15,6 +15,15 @@
 
         bamCorrelate
 
+        #if $mode.modeOpt == "bins":
+            bins
+            --binSize '$mode.binSize'
+            --numberOfSamples '$mode.numberOfSamples'
+        #else:
+            BED-file
+            --BED $mode.region_file
+        #end if
+
         @THREADS@
 
         --bamfiles #echo " ".join($files)
@@ -31,13 +40,6 @@
             --outFileCorMatrix '$outFileCorMatrix'
         #end if
 
-        #if $mode.modeOpt == "bins":
-            --binSize '$mode.binSize'
-            --numberOfSamples '$mode.numberOfSamples'
-        #else:
-            --BED $mode.region_file
-        #end if
-
         ## options available in both modes
         #if $mode.advancedOpt.showAdvancedOpt == "yes":