# HG changeset patch
# User modencode-dcc
# Date 1358553699 18000
# Node ID 2db63ab9b129be5a2bef26c007b6526c75356970
# Parent  cbbc26d6ca30e8a1a156144be1ca686414dbae7f
Uploaded

diff -r cbbc26d6ca30 -r 2db63ab9b129 spp_wrapper.py
--- a/spp_wrapper.py	Fri Jan 18 18:48:21 2013 -0500
+++ b/spp_wrapper.py	Fri Jan 18 19:01:39 2013 -0500
@@ -36,14 +36,14 @@
     #set additional options
     #========================================================================================
     if (options['action'] == "cross_correlation"):
-    cmdline = "%s %s %s %s > default_output.txt" % ( cmdline, options['savp'], options['out'], options['rf'] ) 
+        cmdline = "%s %s %s %s > default_output.txt" % ( cmdline, options['savp'], options['out'], options['rf'] ) 
     elif (options['action'] == "peak_calling"):
-    cmdline = "%s -fdr=%s -npeak=%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['fdr'], options['npeak'], options['savr'], options['savd'], options['savn'], options['savp'], options['rf'] ) 
+        cmdline = "%s -fdr=%s -npeak=%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['fdr'], options['npeak'], options['savr'], options['savd'], options['savn'], options['savp'], options['rf'] ) 
     elif (options['action'] == "idr"):
-    cmdline = "%s -npeak=%s %s %s %s %s > default_output.txt" % ( cmdline, options['npeak'], options['savr'], options['savp'], options['out'], options['rf'] ) 
+        cmdline = "%s -npeak=%s %s %s %s %s > default_output.txt" % ( cmdline, options['npeak'], options['savr'], options['savp'], options['out'], options['rf'] ) 
     elif (options['action'] == "custom"):
-    cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] )
-    cmdline = "%s %s  %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] )
+        cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] )
+        cmdline = "%s %s  %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] )
 
     #run cmdline
     #========================================================================================