def add_options_to_parser(p):
from pbreports.io.validators import validate_file
p.description = __doc__ # FIXME which is probably wrong
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("basemods_h5", help="modifications.h5", type=validate_file)
p.set_defaults(func=_args_runner)
return p
def add_options_to_parser(p):
from pbreports.io.validators import validate_file
p.description = __doc__ # FIXME which is probably wrong
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("basemods_h5", help="modifications.h5", type=validate_file)
p.set_defaults(func=_args_runner)
return p
def add_options_to_parser(p):
desc = 'Generates a report showing control quality and readlength information.'
p.description = desc
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("cntrCmpH5", help="control_reads.cmp.h5", type=validate_file)
p.add_argument("csv", help="filtered_summary.csv", type=validate_file)
p.set_defaults(func=args_runner)
return p
def add_options_to_parser(p):
desc = spec.description
p.description = desc
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("cntrCmpH5", help="control_reads.cmp.h5",
type=validate_file)
p.add_argument("csv", help="filtered_summary.csv", type=validate_file)
p.set_defaults(func=args_runner)
return p
def add_options_to_parser(p):
desc = 'Generates a report showing control quality and readlength information.'
p.description = desc
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("cntrCmpH5",
help="control_reads.cmp.h5",
type=validate_file)
p.add_argument("csv", help="filtered_summary.csv", type=validate_file)
p.set_defaults(func=args_runner)
return p
def add_options_to_parser(p):
desc = 'Generates a report showing coverage plots for the top 25 contigs of the supplied reference.'
p.description = desc
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("reference", help="reference file or directory", type=str)
p.add_argument("gff", help="alignment_summary.gff", type=validate_file)
p.add_argument("--maxContigs", action="store", default=25,
help="Max number of contigs to plot. Defaults to 25.")
p.set_defaults(func=args_runner)
return p
def add_options_to_parser(p):
desc = spec.description
p.description = desc
p.version = __version__
p = add_base_and_plot_options(p)
p.add_argument("cntrCmpH5",
help="control_reads.cmp.h5",
type=validate_file)
p.add_argument("csv", help="filtered_summary.csv", type=validate_file)
p.set_defaults(func=args_runner)
return p
