def METHOD_NAME(args):
  if (len(args) == 0 or "--help" in args or "--h" in args or "-h" in args):
    raise Usage(usage())
  import iotbx.pdb
  import iotbx.phil
  master_phil = get_master_phil()
  args = list(args)
  input_objects = iotbx.phil.process_command_line_with_files(
    args=args,
    master_phil=master_phil,
    pdb_file_def="analyze_peptides.pdb")
  work_params = input_objects.work.extract()
  if len(work_params.analyze_peptides.pdb) != 1:
    raise Usage(usage())
  file_name = work_params.analyze_peptides.pdb[0]
  pdb_io = iotbx.pdb.input(file_name)
  pdb_hierarchy = pdb_io.construct_hierarchy()
  pdb_hierarchy.reset_i_seq_if_necessary()
  cis_peptides, trans_peptides, outliers = \
    analyze(pdb_hierarchy=pdb_hierarchy)
  show(cis_peptides=cis_peptides,
       trans_peptides=trans_peptides,
       outliers=outliers,
       cis_only=work_params.analyze_peptides.cis_only)