Command Line Arguments are mispositioned

[aziz-zafar]

Hi,

I am using the CLI for your tool. Initially, I was using the command exactly how it has been outlined in the Github. However, upon looking into your cli.py, you can see that

parser = argparse.ArgumentParser(
        prog="gemcat",
        description="GEMCAT tool for metabolomics predictions",
    )

    parser.add_argument(
        "modelfile",
        help=f"Path to model file to use (XML/SBML, JSON, or MAT format), or one of: {model_manager.get_managed_models_str()}",
    )
    parser.add_argument(
        "expressionfile", help="Path to file containing the condition expression data"
    )

    parser.add_argument(
        "-e",
        "--expressioncolumn",
        help="Name of the column containing the condition expression data",
    )

The model file is in fact before the expression file (not the opposite). Could you kindly correct the docs or the code to ensure congruency?

Many thanks,
Aziz

[sauter-roland]

Hi Aziz!

You're right. Thank you for pointing that out!
The following PR should fix the issue: #48

Have a great day and let us know if anything else pops up or you need support.