--- a/multigps.py	Mon Apr 03 13:38:23 2017 -0400
+++ b/multigps.py	Mon Apr 03 14:07:14 2017 -0400
@@ -25,7 +25,7 @@
 parser.add_argument('--format', dest='format', default=None, help='Input expt file data format')
 parser.add_argument('--gaussmodelsmoothing', dest='gaussmodelsmoothing', default=None, help='Use Gaussian model smoothing')
 parser.add_argument('--gausssmoothparam', dest='gausssmoothparam', type=int, default=None, help='Smoothing factor')
-parser.add_argument('--input_item', dest='input_items', action='append', nargs=7, default=None, help="Input files, attributes and options")
+parser.add_argument('--input_item', dest='input_items', action='append', nargs=8, default=None, help="Input files, attributes and options")
 parser.add_argument('--jointinmodel', dest='jointinmodel', default=None, help='Allow joint events in model updates')
 parser.add_argument('--mappability', dest='mappability', type=float, default=None, help='Fraction of the genome that is mappable for these experiments')
 parser.add_argument('--maxtrainingrounds', dest='maxtrainingrounds', type=int, default=None, help='Maximum number of training rounds for updating binding event read distributions')
@@ -66,11 +66,14 @@
 
 
 def generate_design_file(input_items):
+    control_file_names = []
     design_file = open(DESIGN_FILE, 'w')
     for item in input_items:
-        file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item
+        experiment_file_name, control_file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item
+        if control_file_name not in ['None', None, '']:
+            control_file_names.append(control_file_name)
         file_format = file_format.upper()
-        items = [file_name, label, file_format, condition_name]
+        items = [experiment_file_name, label, file_format, condition_name]
         if replicate_name not in ['None', None, '']:
             items.append(replicate_name)
         if experiment_type not in ['None', None, '']:
@@ -79,6 +82,7 @@
             items.append(fixed_read_count)
         design_file.write('%s\n' % '\t'.join(items))
     design_file.close()
+    return control_file_names
 
 
 def get_file_with_extension(dir, ext):
@@ -141,8 +145,10 @@
     cmd += ' --meme1proc'
 # Experiment.
 if args.input_items is not None:
-    generate_design_file(args.input_items)
+    control_file_names = generate_design_file(args.input_items)
     cmd += ' --design %s' % DESIGN_FILE
+    if len(control_file_names) > 0:
+        cmd += ' --ctrl %s' % ','.join(control_file_names)
 else:
     if args.expt is not None:
         cmd += ' --expt %s' % args.expt