def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-rl', '--read_length',
help='The length of reads.',
type=int,
choices=['32', '36', '40', '50', '58', '72', '76', '100'],
default='100',
required=False)
ap.add_argument('--umi',
help='Treat fastqs as having UMI flags embedded.',
action='store_true',
required=False)
ap.add_argument('--no_hotspot',
help='Stop before calling hotspots (default: include all steps).',
action='store_true',
required=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self, parse=False)
ap.add_argument('-a',
'--annotation',
help="Label of annotation (default: '" +
self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2', 'M3', 'M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
"""Parse the input arguments."""
ap = Launch.get_args(self, parse=False)
ap.add_argument(
"-a",
"--annotation",
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, "M2", "M3", "M4"],
default=self.ANNO_DEFAULT,
required=False,
)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
ap.add_argument('--no_tophat',
help='Do not include TopHat steps in pipeline (default: include TopHat steps).',
action='store_true',
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self, parse=False)
ap.add_argument('-a',
'--annotation',
help="Label of annotation (default: '" +
self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2', 'M3', 'M4'],
default=self.ANNO_DEFAULT,
required=False)
ap.add_argument(
'--no_tophat',
help=
'Do not include TopHat steps in pipeline (default: include TopHat steps).',
action='store_true',
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-rl', '--read_length',
help='The length of reads.',
type=int,
choices=['32', '36', '40', '50', '58', '72', '76', '100'],
default='100',
required=False)
ap.add_argument('--umi',
help='Treat fastqs as having UMI flags embedded.',
action='store_true',
required=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
