--- a/tomo_setup.py	Thu Jul 28 17:14:36 2022 +0000
+++ b/tomo_setup.py	Thu Jul 28 17:26:54 2022 +0000
@@ -68,13 +68,17 @@
     print(f'inputfiles ({type(args.inputfiles)}):\n{args.inputfiles}')
     print(f'inputfile_types ({type(args.inputfile_types)}):\n{args.inputfile_types}')
     if isinstance(args.inputfile_types, list):
-        if args.inputfile_types[0] == 'collection':
-            input_as_collection = True
-            if len(args.inputfiles) != 1 or args.inputfiles[0] != inputfiles.txt:
+        if if len(args.inputfile_types) == 1 and args.inputfile_types[0] == 'collection':
+            if len(args.inputfiles) != 1 or args.inputfiles[0] != 'inputfiles.txt':
                 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+
                         f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+
                         f'inputfile_types ({type(inputfile_types)}):\n{inputfile_types}')
+            input_as_collection = True
         else:
+            if len(args.inputfiles) != len(args.inputfile_types):
+                raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+
+                        f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+
+                        f'inputfile_types ({type(inputfile_types)}):\n{inputfile_types}')
             input_as_collection = False
     else:
         raise ValueError(f'Invalid args.inputfile_types: {args.inputfile_types} '+
@@ -84,7 +88,7 @@
     collections = []
     if input_as_collection:
         # Read input file collections and collect data files info
-        with open(args.inputfiles) as cf:
+        with open(args.inputfiles[0]) as cf:
             for line in cf:
                 if not line.strip() or line.startswith('#'):
                     continue