https://github.com/galaxyproject/ephemeris/blob/c6aea18059bdbf405a900288a0ff9e5113c5393b/src/ephemeris/shed_tools_args.py#L123 with https://github.com/galaxyproject/ephemeris/blob/master/src/ephemeris/shed_tools.py#L609 means the command line argument default value takes precedence, which is True.
