--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/fromCSVtoCOBRA_beta.py	Thu Sep 11 20:34:30 2025 +0000
@@ -0,0 +1,69 @@
+import os
+import csv
+import cobra
+import pickle
+import argparse
+import pandas as pd
+import utils.general_utils as utils
+from typing import Optional, Tuple, Union, List, Dict
+import logging
+import utils.rule_parsing  as rulesUtils
+import utils.reaction_parsing as reactionUtils
+import utils.model_utils as modelUtils
+
+ARGS : argparse.Namespace
+def process_args(args: List[str] = None) -> argparse.Namespace:
+    """
+    Parse command-line arguments for CustomDataGenerator.
+    """
+
+    parser = argparse.ArgumentParser(
+        usage="%(prog)s [options]",
+        description="Generate custom data from a given model"
+    )
+
+    parser.add_argument("--out_log", type=str, required=True,
+                        help="Output log file")
+
+    parser.add_argument("--input", type=str,
+                        help="Input tabular file")
+    
+    parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
+                        help="Model format (SBML, JSON, MATLAB, YAML)")
+
+    parser.add_argument("--output", type=str,
+                        help="Output model file")
+    
+    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
+                        help="Tool directory (passed from Galaxy as $__tool_directory__)")
+    
+
+
+    return parser.parse_args(args)
+
+###############################- ENTRY POINT -################################
+def main(args:List[str] = None) -> None:
+    """
+    Initializes everything and sets the program in motion based on the fronted input arguments.
+    
+    Returns:
+        None
+    """
+    # get args from frontend (related xml)
+    global ARGS
+    ARGS = process_args(args)
+
+    model = modelUtils.build_cobra_model_from_csv(ARGS.model_upload)
+
+
+    if ARGS.format == "sbml":
+        cobra.io.write_sbml_model(model, ARGS.output)
+    elif ARGS.format == "json":
+        cobra.io.save_json_model(model, ARGS.output)
+    elif ARGS.format == "mat":
+        cobra.io.save_matlab_model(model, ARGS.output)
+    elif ARGS.format == "yaml":
+        cobra.io.save_yaml_model(model, ARGS.output)
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file