Source code for pacbio_data_processing.ui.cl
#######################################################################
#
# Copyright (C) 2021, 2022 David Palao
#
# This file is part of PacBio data processing.
#
# PacBioDataProcessing is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# PacBio data processing is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with PacBioDataProcessing. If not, see <http://www.gnu.org/licenses/>.
#
#######################################################################
"""This module defines the functions to collect user input from the
command line."""
import argparse
from .options import SM_ANALYSIS_OPTS, BAM_FILTER_OPTS
from .common import parse_user_input
from ..constants import (
SM_ANALYSIS_EXE, SM_ANALYSIS_DESC, BAM_FILTER_EXE, BAM_FILTER_DESC,
)
# def old_parse_cl():
# parser.add_argument(
# "-r", "--restart-from-old-dir", metavar="DIR", type=Path,
# help=(
# "continue analysis from a previous (unfinished) one; "
# "%(metavar)s must be the temporary directory remaining from "
# "the old run."
# )
# )
[docs]def parse_cl_sm_analysis():
return parse_user_input(
argparse.ArgumentParser,
SM_ANALYSIS_EXE, SM_ANALYSIS_DESC, SM_ANALYSIS_OPTS
)
[docs]def parse_cl_bam_filter():
return parse_user_input(
argparse.ArgumentParser,
BAM_FILTER_EXE, BAM_FILTER_DESC, BAM_FILTER_OPTS
)