diff ebcsgen_sbml_export.py @ 0:2f3f67415022 draft

planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
author sybila
date Sat, 08 Oct 2022 12:55:26 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ebcsgen_sbml_export.py	Sat Oct 08 12:55:26 2022 +0000
@@ -0,0 +1,30 @@
+import argparse
+
+from eBCSgen.Errors.ModelParsingError import ModelParsingError
+from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
+from eBCSgen.Parsing.ParseBCSL import Parser
+
+import libsbml
+
+
+args_parser = argparse.ArgumentParser(description='Export SBML model with usage of SBML-multi package')
+
+args_parser._action_groups.pop()
+required = args_parser.add_argument_group('required arguments')
+
+required.add_argument('--model', type=str, required=True)
+required.add_argument('--output', type=str, required=True)
+
+args = args_parser.parse_args()
+
+model_parser = Parser("model")
+model_str = open(args.model, "r").read()
+
+model = model_parser.parse(model_str)
+if model.success:
+    document = model.data.export_sbml()
+    libsbml.writeSBMLToFile(document, args.output)
+else:
+    if "error" in model.data:
+        raise UnspecifiedParsingError(model.data["error"])
+    raise ModelParsingError(model.data, model_str)