text: from argparse  import ArgumentParser
  from rptools._version import __version__
  
  
  def add_arguments(parser):
      parser.add_argument(
          'pathway_file',
          type=str,
          help='SBML file that contains an heterologous pathway'
      )
      parser.add_argument(
          'model_file',
          type=str,
          help='GEM model file (SBML)'
      )
      parser.add_argument(
          'compartment_id',
          type=str,
          help='model compartment id to consider (e.g. \'c\' or \'MNXC3\' or \'c|MNXC3|cytosol|cytoplasm\')'
      )
      parser.add_argument(
          'outfile',
          type=str,
          help='output file'
      )
      parser.add_argument(
          '--objective_rxn_id',
          type=str,
          default='rxn_target',
          help='reaction ID to optimise (default: rxn_target)'
      )
      parser.add_argument(
          '--biomass_rxn_id',
          type=str,
          default='biomass',
          help='biomass reaction ID (default: biomass). Note: Only for \'fraction\' simulation'
      )
      parser.add_argument(
          '--sim',
          type=str,
          choices=['fba', 'pfba', 'fraction'],
          default='fraction',
          help='type of simulation to use (default: fraction)'
      )
      parser.add_argument(
          '--fraction_of',
          type=float,
          default=0.75,
          help='fraction of the optimum (default: 0.75). Note: this value is ignored is \'fba\' is used'
      )
      parser.add_argument(
          '--merge',
          action='store_true',
          default=False,
          help='output the full merged model instead of heterologous pathway only (default: False)'
      )
      parser.add_argument(
          '--ignore_orphan_species',
          action='store_true',
          default=True,
          help='ignore metabolites that are only consumed or produced (default: True)'
      )
      return parser
  