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def parse_arguments():
"""
Creat parser instance and parse command-line arguments passed to the pipeline
:return argparse.Namespace: parsed arguments namespace
"""
parser = VersionInHelpParser(prog="PEPATAC_collator",
description='PEPATAC collator' , version=__version__)
parser = pypiper.add_pypiper_args(parser, groups=['pypiper', 'looper'])
parser.add_argument("-n", "--name",
help="Name of the project to use.", type=str)
parser.add_argument("-r", "--results",
help="Output results sub directory path.", type=str)
args = parser.parse_args()
return args
def build_argparser():
"""
Builds argument parser.
:return argparse.ArgumentParser
"""
banner = "%(prog)s - reference genome asset manager"
additional_description = "\nhttps://refgenie.databio.org"
parser = VersionInHelpParser(
prog="refgenie",
version=__version__,
description=banner,
epilog=additional_description)
subparsers = parser.add_subparsers(dest="command")
def add_subparser(cmd, description):
return subparsers.add_parser(
cmd, description=description, help=description)
sps = {}
for cmd, desc in SUBPARSER_MESSAGES.items():
sps[cmd] = add_subparser(cmd, desc)
# It's required for init
sps[cmd].add_argument(
def build_argparser():
banner = "%(prog)s - Interact with PEPs"
additional_description = "\nhttp://peppy.databio.org/"
parser = VersionInHelpParser(
prog=PKG_NAME,
description=banner,
epilog=additional_description,
version=__version__)
subparsers = parser.add_subparsers(dest="command")
sps = {}
for cmd, desc in SUBPARSER_MSGS.items():
sps[cmd] = subparsers.add_parser(cmd, description=desc, help=desc)
sps[cmd].add_argument('pep', metavar="PEP",
help="Path to a PEP configuration "
"file in yaml format.")
sps[VALIDATE_CMD].add_argument("-s", "--schema", required=True,
help="Path to a PEP schema file in yaml format.")