Python argparse.RawDescriptionHelpFormatter() Examples

def build_arg_parser(description, env_vars={}):
    from argparse import ArgumentParser, RawDescriptionHelpFormatter
    from textwrap import dedent

    base_env_vars = {
        'MONO_SOURCE_ROOT': 'Overrides default value for --mono-sources',
    }

    env_vars_text = '\n'.join(['    %s: %s' % (var, desc) for var, desc in env_vars.items()])
    base_env_vars_text = '\n'.join(['    %s: %s' % (var, desc) for var, desc in base_env_vars.items()])

    epilog=dedent('''\
environment variables:
%s
%s
''' % (env_vars_text, base_env_vars_text))

    return ArgumentParser(
        description=description,
        formatter_class=RawDescriptionHelpFormatter,
        epilog=epilog
    ) 

def parse_args(self):
        parser = argparse.ArgumentParser(
            description = self._description,
            epilog = self._epilog, 
            formatter_class = argparse.RawDescriptionHelpFormatter,
            usage = self._usage)

        self._add_flags(parser)
        self._add_export(parser)

        ### Print help message if no arguments are present.
        if len(sys.argv[1:]) == 0:
            parser.print_help()
            raise SystemExit

        args = parser.parse_args()
        return args, parser 

def create_parser():
    parser = ArgumentParser(description=__doc__,
                            formatter_class=RawDescriptionHelpFormatter)
    parser.add_argument('--debug', action='store_true')
    parser.add_argument('--delimiter')
    parser.add_argument('--embedding-size', default=200, type=int)
    parser.add_argument('--graph-path')
    parser.add_argument('--has-header', action='store_true')
    parser.add_argument('--input', '-i', dest='infile', required=True)
    parser.add_argument('--log-level', '-l', type=str.upper, default='INFO')
    parser.add_argument('--num-walks', default=1, type=int)
    parser.add_argument('--model', '-m', dest='model_path')
    parser.add_argument('--output', '-o', dest='outfile', required=True)
    parser.add_argument('--stats', action='store_true')
    parser.add_argument('--undirected', action='store_true')
    parser.add_argument('--walk-length', default=10, type=int)
    parser.add_argument('--window-size', default=5, type=int)
    parser.add_argument('--workers', default=multiprocessing.cpu_count(),
                        type=int)
    return parser 

def create_parser():
    """Set up parsing for command-line arguments
    """
    parser = argparse.ArgumentParser(description=__doc__,  # Use text from file summary up top
                        formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('--reference-cluster-path',
                    dest='ref_cluster_path',
                    help='Path to SCP cluster file to use as reference ' +
                    '(i.e. normal, control) cells')
    parser.add_argument('--reference-group-name',
                    dest='ref_group_name',
                    help='Name of cell group in SCP cluster file to use as ' +
                    'label for inferCNV references')
    parser.add_argument('--metadata-path',
                    help='Path to SCP metadata file that contains all cells')
    parser.add_argument('--observation-group-name',
                    dest='obs_group_name',
                    help='Name of the cell group in SCP metadata file to ' +
                    'use as label for observations')
    parser.add_argument('--delimiter',
                    help='Delimiter in SCP cluster file',
                    default="\t")
    parser.add_argument('--output-dir',
                    help='Path to write output')
    return parser 

def _create_parser():
    parser = ArgumentParser(description="Compare two tempest xml results",
                            formatter_class=RawDescriptionHelpFormatter)
    parser.add_argument("result_1",
                        help="path to xml result 1")
    parser.add_argument("result_2",
                        help="path to xml result 2")
    '''TODO future functionality
    parser.add_argument("-c", "--csv", dest="output_csv",
                        action="store_true",
                        help="output csv")
    parser.add_argument("-m", "--html", dest="output_html",
                        action="store_true",
                        help="output html")
    parser.add_argument("-n", "--json", dest="output_json",
                        action="store_true",
                        help="output json")
    parser.add_argument("-o", "--output-file", dest="output_file",
                        type=str, required=False,
                        help="If specified, output will be saved to given "
                        "file")
    '''
    return parser 

def __init__(self, config='config.yaml', description=None):
        super(BaseOptions, self).__init__()
        logging.debug('BaseOptions.__init__')
        self._ordered_keys = []
        self._exclude_keys = set()

        self._parent = argparse.ArgumentParser(add_help=False)
        self._parser = argparse.ArgumentParser(parents=[self._parent],
                                               description=description,
                                               formatter_class=argparse.RawDescriptionHelpFormatter)

        # config file option
        self.config = config

        # config file
        self._parent.add_argument('--config', type=str, default=self.config, metavar=self.config,
                                  help='configuration file name') 

def create_parser(prog):
  """Create an argument parser, adding in the list of providers."""
  parser = argparse.ArgumentParser(
      prog=prog, formatter_class=argparse.RawDescriptionHelpFormatter)

  parser.add_argument(
      '--provider',
      default='google-v2',
      choices=['local', 'google-v2', 'google-cls-v2', 'test-fails'],
      help="""Job service provider. Valid values are "google-v2" (Google's
        Pipeline API v2alpha1), "google-cls-v2" (Google's Pipelines API v2beta)
        and "local" (local Docker execution).
        "test-*" providers are for testing purposes only.
        (default: google-v2)""",
      metavar='PROVIDER')

  return parser 

def _parse_cli_options():
    """
    Parse command line options, returning `parse_args` from `ArgumentParser`.
    """
    parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter,
                            usage="python %(prog)s <options>",
                            epilog="example:\n"
                                   "python %(prog)s -w workflow1 workflow2 -l my_panel_label\n"
                                   "Christophe Antoniewski <drosofff@gmail.com>\n"
                                   "https://github.com/ARTbio/ansible-artimed/tree/master/scritps/galaxykickstart_from_workflow.py")
    parser.add_argument('-w', '--workflow',
                        dest="workflow_files",
                        required=True,
                        nargs='+',
                        help='A space-separated list of galaxy workflow description files in json format', )
    parser.add_argument('-l', '--panel_label',
                        dest='panel_label',
                        default='Tools from workflows',
                        help='The name of the panel where the tools will show up in Galaxy.'
                             'If not specified: "Tools from workflows"')
    return parser.parse_args() 

def create_parser():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="learn BPE-based word segmentation")

    parser.add_argument(
        '--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
        metavar='PATH',
        help="Input file (default: standard input).")
    parser.add_argument(
        '--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
        required=True,
        help="File with BPE codes (created by learn_bpe.py).")
    parser.add_argument(
        '--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
        metavar='PATH',
        help="Output file (default: standard output)")
    parser.add_argument(
        '--separator', '-s', type=str, default='@@', metavar='STR',
        help="Separator between non-final subword units (default: '%(default)s'))")

    return parser 

def create_parser():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="learn BPE-based word segmentation")

    parser.add_argument(
        '--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
        metavar='PATH',
        help="Input text (default: standard input).")
    parser.add_argument(
        '--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
        metavar='PATH',
        help="Output file for BPE codes (default: standard output)")
    parser.add_argument(
        '--symbols', '-s', type=int, default=10000,
        help="Create this many new symbols (each representing a character n-gram) (default: %(default)s))")
    parser.add_argument(
        '--min-frequency', type=int, default=2, metavar='FREQ',
        help='Stop if no symbol pair has frequency >= FREQ (default: %(default)s))')
    parser.add_argument(
        '--verbose', '-v', action="store_true",
        help="verbose mode.")

    return parser 

def add_list_blocks_parser(subparsers, parent_parser):
    """Creates the arg parsers needed for the compare command.
    """
    parser = subparsers.add_parser(
        'list-blocks',
        help='List blocks from different nodes.',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog='',
        parents=[parent_parser, base_multinode_parser()])

    parser.add_argument(
        '-n',
        '--count',
        default=10,
        type=int,
        help='the number of blocks to list') 

def doArchive(argv, bobRoot):
    subHelp = "\n          ... ".join(sorted(
        [ "{:8} {}".format(c, d[1]) for (c, d) in availableArchiveCmds.items() ]))
    parser = argparse.ArgumentParser(prog="bob archive",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="""Manage binary artifacts archive. The following subcommands are available:

  bob archive {}
""".format(subHelp))
    parser.add_argument('subcommand', help="Subcommand")
    parser.add_argument('args', nargs=argparse.REMAINDER,
                        help="Arguments for subcommand")

    args = parser.parse_args(argv)

    if args.subcommand in availableArchiveCmds:
        availableArchiveCmds[args.subcommand][0](args.args)
    else:
        parser.error("Unknown subcommand '{}'".format(args.subcommand)) 

def run():
    parser = argparse.ArgumentParser(description="""
    The SafeLife command-line tool can be used to interactively play
    a game of SafeLife, print procedurally generated SafeLife boards,
    or convert saved boards to images for easy viewing.

    Please select one of the available commands to run the program.
    You can run `safelife <command> --help` to get more help on a
    particular command.
    """, formatter_class=argparse.RawDescriptionHelpFormatter)
    subparsers = parser.add_subparsers(dest="cmd", help="Top-level command.")
    interactive_game._make_cmd_args(subparsers)
    render_graphics._make_cmd_args(subparsers)
    args = parser.parse_args()
    if args.cmd is None:
        parser.print_help()
    else:
        args.run_cmd(args) 

def main():
    """ Parse command line arguments and start exploit """
    parser = argparse.ArgumentParser(
            add_help=False,
            formatter_class=argparse.RawDescriptionHelpFormatter,
            epilog="Examples: %(prog)s -t http://192.168.0.1/ -u username -p password -c whoami")

    # Adds arguments to help menu
    parser.add_argument("-h", action="help", help="Print this help message then exit")
    parser.add_argument("-t", dest="target", required="yes", help="Target URL address like: https://localhost:443/")
    parser.add_argument("-u", dest="username", required="yes", help="Username to authenticate")
    parser.add_argument("-p", dest="password", required="yes", help="Password to authenticate")
    parser.add_argument("-c", dest="command", required="yes", help="Shell command to execute")

    # Assigns the arguments to various variables
    args = parser.parse_args()

    run(args.target, args.username, args.password, args.command)


#
# Main
# 

def main():
	import argparse
	
	parser = argparse.ArgumentParser(description='Polls the kerberos service for a TGT for the sepcified user', formatter_class=argparse.RawDescriptionHelpFormatter, epilog = kerberos_url_help_epilog)
	parser.add_argument('kerberos_connection_url', help='the kerberos target string. ')
	parser.add_argument('ccache', help='ccache file to store the TGT ticket in')
	parser.add_argument('-v', '--verbose', action='count', default=0)
	
	args = parser.parse_args()
	if args.verbose == 0:
		logging.basicConfig(level=logging.INFO)
	elif args.verbose == 1:
		logging.basicConfig(level=logging.DEBUG)
	else:
		logging.basicConfig(level=1)
	
	asyncio.run(amain(args)) 

def main():
	import argparse
	
	parser = argparse.ArgumentParser(description='Gets an S4U2proxy ticket impersonating given user', formatter_class=argparse.RawDescriptionHelpFormatter, epilog = kerberos_url_help_epilog)
	parser.add_argument('kerberos_connection_url', help='the kerberos target string in the following format <domain>/<username>/<secret_type>:<secret>@<domaincontroller-ip>')
	parser.add_argument('spn', help='the service principal in format <service>/<server-hostname>@<domain> Example: cifs/fileserver.test.corp@TEST.corp for a TGS ticket to be used for file access on server "fileserver". IMPORTANT: SERVER\'S HOSTNAME MUST BE USED, NOT IP!!!')
	parser.add_argument('targetuser', help='')
	parser.add_argument('ccache', help='ccache file to store the TGT ticket in')
	parser.add_argument('-v', '--verbose', action='count', default=0)
	
	args = parser.parse_args()
	if args.verbose == 0:
		logger.setLevel(logging.WARNING)
	elif args.verbose == 1:
		logger.setLevel(logging.INFO)
	else:
		logger.setLevel(1)

	asyncio.run(amain(args)) 

def main():
	import argparse
	
	parser = argparse.ArgumentParser(description='Polls the kerberos service for a TGS for the sepcified user and specified service', formatter_class=argparse.RawDescriptionHelpFormatter, epilog = kerberos_url_help_epilog)
	parser.add_argument('kerberos_connection_string', help='the kerberos target string in the following format <domain>/<username>/<secret_type>:<secret>@<domaincontroller-ip>')
	parser.add_argument('spn', help='the service principal in format <service>/<server-hostname>@<domain> Example: cifs/fileserver.test.corp@TEST.corp for a TGS ticket to be used for file access on server "fileserver". IMPORTANT: SERVER\'S HOSTNAME MUST BE USED, NOT IP!!!')
	parser.add_argument('ccache', help='ccache file to store the TGT ticket in')
	parser.add_argument('-u', action='store_true', help='Use UDP instead of TCP (not tested)')
	parser.add_argument('-v', '--verbose', action='count', default=0)
	
	args = parser.parse_args()
	if args.verbose == 0:
		logging.basicConfig(level=logging.INFO)
	elif args.verbose == 1:
		logging.basicConfig(level=logging.DEBUG)
	else:
		logging.basicConfig(level=1)
	
	asyncio.run(amain(args)) 

def getfilenames():
    global args
    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
                                     description="Cisco Configuration Analysis Tool",
                                     epilog='Usage example:\n  ccat  smth/config_folder -vlanmap smth/vlanmap_file')
    parser.add_argument("configs", type=str, nargs='?', default=0, help="full path to the configuration file or folder with config(s)")
    parser.add_argument("-vlanmap", type=str, help="path to vlanmap (file that determine how critical is certain vlan, you can find example in 'example' folder)")
    parser.add_argument("-output", type=str, help="path to output html files directory")
    parser.add_argument("--no-console-display", action='store_true', help="to output analysis results in html files directory or into network graph")
    parser.add_argument("--no-ipv6", action='store_true', help="if you're not using IPv6")
    parser.add_argument("--disabled-interfaces", action='store_true', help="check interfaces even if they are turned off")
    parser.add_argument("--storm_level", type=float, help="to set up appropriate level for storm-control (by default value=80)")
    parser.add_argument("--max_number_mac", type=int, help="to set up maximum number of mac-addresses for port-security (by default value=10)")
    parser.add_argument("--dump-creds", action='store_true', help="enable credentials harvesting")
    parser.add_argument("--debug", action='store_true', help="enable debug output")
    graph_group = parser.add_argument_group('Network graph')
    graph_group.add_argument("--graph", type=str, nargs='?', default=0, help="left the argument empty to get into interactive mode or define a file name for graph output in png extension")
    args = parser.parse_args()
    if not(args.configs):
        print ('Usage example:\n  ccat  smth/config_folder -vlanmap smth/vlanmap_file\n\nFor more details try --help')
        exit()
    if args.no_console_display and not args.output and args.graph == 0:
        print('\nYou should define html files directory with -output key OR use --graph key to use this options\n\nFor more details try --help')
        exit()
    return _getargs___arg_parser(args.configs, args.vlanmap) 

def main():
    parser = argparse.ArgumentParser(prog=os.path.basename(sys.argv[0]),
        formatter_class=argparse.RawDescriptionHelpFormatter,
                                     description=__doc__)
    parser.add_argument("input",
                        help="XML wiki dump file")
    parser.add_argument("--id", default="",
                        help="article number, or range first-last")
    parser.add_argument("--template", action="store_true",
                        help="extract also all templates")
    parser.add_argument("-v", "--version", action="version",
                        version='%(prog)s ' + version,
                        help="print program version")

    args = parser.parse_args()

    process_data(args.input, args.id, args.template) 

def parse_arguments():
    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    subparsers = parser.add_subparsers(dest="cmd", required=True)

    subparser = subparsers.add_parser("info", help="view clips and keyframes in an animation file")
    subparser.add_argument("input", help="input file specification")

    subparser = subparsers.add_parser(
        "json", help="convert an animation in FlatBuffers format to JSON format")
    subparser.add_argument("input", help="input file specification")
    subparser.add_argument("-o", "--output", help="output file specification")

    subparser = subparsers.add_parser(
        "bin", help="convert an animation in JSON format to FlatBuffers format.")
    subparser.add_argument("input", help="input file specification")
    subparser.add_argument("-o", "--output", help="output file specification")

    subparser = subparsers.add_parser("images", help="export procedural face images from an animation file")
    subparser.add_argument("input", help="input file specification")
    subparser.add_argument("-p", "--prefix", help="output file specification prefix")

    args = parser.parse_args()
    return args 

def setup_parser():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description=textwrap.dedent(__doc__.strip()),
        add_help=False)

    parser.add_argument('-c', '--config',
                        help='Config file.', required=True)
    # "-d" currently unused
    parser.add_argument('-d', '--debug',
                        help='Show debug messages.', action='store_true')
    parser.add_argument('-h', '--help',
                        help='Show this screen.', action='help')
    parser.add_argument('-l', '--log_config',
                        help='Log config file\'s path.', required=True)
    parser.add_argument('-p', '--spark_path',
                        help='Spark\'s path.', required=True)
    parser.add_argument('-s', '--sources',
                        help='A list of data sources.', nargs='*')
    parser.add_argument('-v', '--version',
                        help='Show version.', action='version',
                        version=setup_property.VERSION)

    return parser 

def parse_and_run():
  """Parses the command line and runs the chosen subcommand.

  Returns the command's return value (either int or None, suitable as input to
  `os._exit`).
  """
  parser = argparse.ArgumentParser(
      description='Interact with the recipe system.')

  _add_common_args(parser)

  subp = parser.add_subparsers(dest='command')
  for module in _COMMANDS:
    description = module.__doc__
    helplines = []
    for line in description.splitlines():
      line = line.strip()
      if not line:
        break
      helplines.append(line)
    module.add_arguments(subp.add_parser(
        module.__name__.split('.')[-1],  # use module's short name
        formatter_class=argparse.RawDescriptionHelpFormatter,
        help=' '.join(helplines),
        description=description,
    ))

  args = parser.parse_args()
  _common_post_process(args)
  args.postprocess_func(parser.error, args)

  return args.func(args) 

def main():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description=__doc__
    )
    parser.add_argument("fonts", nargs="+", help=(
            "Paths to font files. Fonts must be part of the same family."
        )
    )
    args = parser.parse_args()
    fonts = args.fonts

    # This monstrosity exists so we don't break the v1 api.
    italic_font = None
    if len(fonts) > 2:
        raise Exception(
            "Can only add STAT tables to a max of two fonts. "
            "Run gftools fix-vf-meta --help for usage instructions"
        )
    elif len(fonts) == 2:
        if "Italic" in fonts[0]:
            italic_font = TTFont(fonts[0])
            roman_font = TTFont(fonts[1])
        elif "Italic" in fonts[1]:
            italic_font = TTFont(fonts[1])
            roman_font = TTFont(fonts[0])
        else:
            raise Exception("No Italic font found!")
    else:
        roman_font = TTFont(fonts[0])
    update_nametable(roman_font)
    if italic_font:
        update_nametable(italic_font)
    build_stat(roman_font, italic_font)
    roman_font.save(roman_font.reader.file.name + ".fix")
    if italic_font:
        italic_font.save(italic_font.reader.file.name + ".fix") 

def __main__(argv):
    """Command Line parser for sort_sparse_matrix
    Inputs-
    command line arguments
    """
    # create the argument parser
    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    # add arguments
    parser.add_argument('matrix_file', help='Sparse Matrix file')
    parser.add_argument('--sorted_matrix_file', '-o', help='Gene sorted sparse matrix file path', default=None)
    # call sort_sparse_matrix with parsed args
    args = parser.parse_args()
    sort_sparse_matrix(matrix_file=args.matrix_file, sorted_matrix_file=args.sorted_matrix_file)

# python default 

def create_parser():
    """Set up parsing for command-line arguments
    """
    parser = ArgumentParser(description=__doc__,  # Use text from file summary up top
                        formatter_class=RawDescriptionHelpFormatter)
    parser.add_argument('--matrix-path',
                    help='Path to expression matrix file')
    parser.add_argument('--matrix-delimiter',
                    help='Delimiter in expression matrix',
                    default='\t')
    parser.add_argument('--gen-pos-file',
                    help='Path to gen_pos.txt genomic positions file from inferCNV')
    parser.add_argument('--cluster-names',
                    help='Names of cluster groups',
                    nargs='+')
    parser.add_argument('--reference-group-name',
                    dest='ref_group_name',
                    help='Name of cell group in SCP cluster file to use as ' +
                    'label for inferCNV references')
    parser.add_argument('--ref-cluster-names',
                    help='Names of reference (normal) cluster groups',
                    nargs='+', default=[])
    parser.add_argument('--ordered-labels',
                    help='Sorted labels for clusters',
                    nargs='+', default=[])
    parser.add_argument('--heatmap-thresholds-path',
                    help='Path to heatmap thresholds file', required=False)
    # parser.add_argument('--ref-heatmap-thresholds',
    #                 help='Numeric thresholds for heatmap of reference (normal) cluster groups',
    #                 nargs='+', required=False)
    parser.add_argument('--cluster-paths',
                    help='Path or URL to cluster group files',
                    nargs='+')
    parser.add_argument('--metadata-path',
                    help='Path or URL to metadata file')
    parser.add_argument('--output-dir',
                    help='Path to write output')

    return parser 

def parse_args(args):
    """
    Takes in the command-line arguments list (args), and returns a nice argparse
    result with fields for all the options.
    Borrows heavily from the argparse documentation examples:
    <http://docs.python.org/library/argparse.html>
    """

    # The command line arguments start with the program name, which we don't
    # want to treat as an argument for argparse. So we remove it.
    args = args[1:]

    # Construct the parser (which is stored in parser)
    # Module docstring lives in __doc__
    # See http://python-forum.com/pythonforum/viewtopic.php?f=3&t=36847
    # And a formatter class so our examples in the docstring look good. Isn't it
    # convenient how we already wrapped it to 80 characters?
    # See http://docs.python.org/library/argparse.html#formatter-class
    parser = argparse.ArgumentParser(description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter)

    # Now add all the options to it
    parser.add_argument("avdl", type=argparse.FileType('r'),
        help="the AVDL file to read")

    return parser.parse_args(args) 

def create_parser():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="learn BPE-based word segmentation")

    parser.add_argument(
        '--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
        metavar='PATH',
        help="Input file (default: standard input).")
    parser.add_argument(
        '--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
        required=True,
        help="File with BPE codes (created by learn_bpe.py).")
    parser.add_argument(
        '--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
        metavar='PATH',
        help="Output file (default: standard output)")
    parser.add_argument(
        '--separator', '-s', type=str, default='@@', metavar='STR',
        help="Separator between non-final subword units (default: '%(default)s'))")
    parser.add_argument(
        '--vocabulary', type=argparse.FileType('r'), default=None,
        metavar="PATH",
        help="Vocabulary file (built with get_vocab.py). If provided, this script reverts any merge operations that produce an OOV.")
    parser.add_argument(
        '--vocabulary-threshold', type=int, default=None,
        metavar="INT",
        help="Vocabulary threshold. If vocabulary is provided, any word with frequency < threshold will be treated as OOV")
    parser.add_argument(
        '--glossaries', type=str, nargs='+', default=None,
        metavar="STR",
        help="Glossaries. The strings provided in glossaries will not be affected"+
             "by the BPE (i.e. they will neither be broken into subwords, nor concatenated with other subwords")

    return parser 

def create_parser():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="learn BPE-based word segmentation")

    parser.add_argument(
        '--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
        metavar='PATH',
        help="Input text (default: standard input).")

    parser.add_argument(
        '--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
        metavar='PATH',
        help="Output file for BPE codes (default: standard output)")
    parser.add_argument(
        '--symbols', '-s', type=int, default=10000,
        help="Create this many new symbols (each representing a character n-gram) (default: %(default)s))")
    parser.add_argument(
        '--min-frequency', type=int, default=2, metavar='FREQ',
        help='Stop if no symbol pair has frequency >= FREQ (default: %(default)s))')
    parser.add_argument('--dict-input', action="store_true",
        help="If set, input file is interpreted as a dictionary where each line contains a word-count pair")
    parser.add_argument(
        '--verbose', '-v', action="store_true",
        help="verbose mode.")

    return parser 

def __init__(self):
        self.work = os.getcwd()
        self.python = shutil.which('python3')
        self.project_path = os.path.join(os.path.dirname(os.path.abspath(__file__)))
        self.package_name = 'pydarkstar'
        self.package_path = os.path.join(self.project_path, self.package_name)
        self.apps_path = os.path.join(self.package_path, 'apps')
        self.bin_path = os.path.join(self.project_path, 'bin')
        self.apps_list = {
            'broker': 'pydarkstar.apps.broker.run',
            'seller': 'pydarkstar.apps.seller.run',
            'buyer': 'pydarkstar.apps.buyer.run',
            'refill': 'pydarkstar.apps.refill.run',
            'clear': 'pydarkstar.apps.clear.run',
            'scrub': 'pydarkstar.apps.scrub.run',
            'alter': 'pydarkstar.apps.alter.run',
        }

        if self.python is None:
            self.python = 'python'

        log_parameter('work', self.work)
        log_parameter('project_path', self.project_path)
        log_parameter('package_name', self.package_name)
        log_parameter('package_path', self.package_path)
        log_parameter('python', self.python)
        log_parameter('bin_path', self.bin_path)

        parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
        parser.parse_args()

        try:
            assert os.path.exists(self.work)
            assert os.path.exists(self.project_path)
            assert os.path.exists(self.package_path)
            assert os.path.exists(self.apps_path)
        except AssertionError:
            logging.exception('invalid configuration')
            exit(-1) 

def _parse_cli_options():
    """
    Parse command line options, returning `parse_args` from `ArgumentParser`.
    """
    parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter,
                            usage="python %(prog)s <options>",
                            epilog="Workflow files must have been exported from Galaxy release 16.04 or newer.\n\n"
                                   "example:\n"
                                   "python %(prog)s -w workflow1 workflow2 -o mytool_list.yml -l my_panel_label\n"
                                   "Christophe Antoniewski <drosofff@gmail.com>\n"
                                   "https://github.com/ARTbio/ansible-artimed/tree/master/extra-files/generate_tool_list_from_ga_workflow_files.py")
    parser.add_argument('-w', '--workflow',
                        dest="workflow_files",
                        required=True,
                        nargs='+',
                        help='A space separated list of galaxy workflow description files in json format', )
    parser.add_argument('-o', '--output-file',
                        required=True,
                        dest='output_file',
                        help='The output file with a yml tool list')
    parser.add_argument('-l', '--panel_label',
                        dest='panel_label',
                        default='Tools from workflows',
                        help='The name of the panel where the tools will show up in Galaxy.'
                             'If not specified: "Tools from workflows"')
    return parser.parse_args()