--- a/COBRAxy/custom_data_generator.py	Wed Nov 06 10:12:52 2024 +0000
+++ b/COBRAxy/custom_data_generator.py	Wed Nov 06 13:57:24 2024 +0000
@@ -6,11 +6,11 @@
 import pandas as pd
 import utils.general_utils as utils
 import utils.rule_parsing  as rulesUtils
-from typing import Optional, Tuple, Union, Dict
+from typing import Optional, Tuple, Union, List, Dict
 import utils.reaction_parsing as reactionUtils
 
 ARGS : argparse.Namespace
-def process_args() -> argparse.Namespace:
+def process_args(args:List[str] = None) -> argparse.Namespace:
     """
     Interfaces the script of a module with its frontend, making the user's choices for
     various parameters available as values in code.
@@ -35,9 +35,8 @@
     parser.add_argument("-id", "--input",   type = str, required = True, help = "Input model")
     parser.add_argument("-mn", "--name",    type = str, required = True, help = "Input model name")
     # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
-    
-    argsNamespace = parser.parse_args()
-    argsNamespace.out_dir = "result"
+    parser.add_argument('-idop', '--output_path', type = str, default='result', help = 'output path for maps')
+    argsNamespace = parser.parse_args(args)
     # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection
 
     return argsNamespace
@@ -184,7 +183,7 @@
             writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })
 
 ###############################- ENTRY POINT -################################
-def main() -> None:
+def main(args:List[str] = None) -> None:
     """
     Initializes everything and sets the program in motion based on the fronted input arguments.
     
@@ -193,10 +192,10 @@
     """
     # get args from frontend (related xml)
     global ARGS
-    ARGS = process_args()
+    ARGS = process_args(args)
 
     # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this!
-    if os.path.isdir(ARGS.out_dir) == False: os.makedirs(ARGS.out_dir)
+    if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path)
 
     # load custom model
     model = load_custom_model(