--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MergeFilesWrapper.py	Wed Aug 03 15:14:17 2016 -0400
@@ -0,0 +1,11 @@
+import sys
+import os
+
+infile1 = sys.argv[1] # scaffold report #1 -- filename
+infile2 = sys.argv[2] # scaffold report #2 -- filename
+infile3 = sys.argv[3] # scaffold report #3 -- filename or "False"
+baitfile = sys.argv[4] # Bait file -- filename
+outfile = sys.argv[5] # output filename
+ins_path = sys.argv[6]
+
+cmd = r"python " + str(ins_path) + " " + str(infile1) + " " + str(infile2) + " " + str(infile3) + " " + str(baitfile) + " " str(outfile)