Parameters

ModelPolisher provides various command-line options which can be printed using the following command:

java -jar <path>/ModelPolisher-noDB-CURRENT_VERSION.jar -? 

Here is a list of mostly used options which we recommend to any general user:

• --input=<input>: Provide the path to your input model to be polished. You can also provide a path to directory containing multiple models.
• --output=<output>: Provide the path to the output file or directory to write polished models. Directory/File is created if not already present.
• --annotate-with-bigg=true: Adds annotations from BiGGDB. Note: User needs to set-up Postgres database in advance.
  • User needs to provide --bigg-host=<string>, --bigg-port=<decimal integer>, --bigg-user=<string>, --bigg-passwd=<string>, --bigg-dbname=<string> if not using default docker containers to run ModelPolisher.
• --add-adb-annotations=true: Annotations will be added to species and reactions from AnnotateDB also. Effective only if 'annotate-with-bigg' is true.
  • User needs to provide --adb-host=<string>, --adb-port=<decimal integer>, --adb-user=<string>, --adb-passwd=<string>, --adb-dbname=<string> if not using default docker containers to run ModelPolisher.
• --output-combine=true: Produce output as a single COMBINE Archive including polished model and glossary rdf file. NOTE: Output file name is taken from input to option --output.