def _add_run_random_fastq_options(p):
add_log_debug_option(p)
p.add_argument('--max-records',
type=int,
default=1000,
help="Max number of Fasta record to write.")
U.add_fastq_output(p)
return p
def _add_run_fasta_filter_options(p):
add_log_debug_option(p)
p.add_argument('--min-length',
type=int,
default=150,
help='Min Length of Sequence to filter')
U.add_fasta_input(p)
U.add_fasta_output(p)
return p
def _add_run_random_fofn_options(p):
add_log_debug_option(p)
U.add_output_dir_option(p)
p.add_argument('--nfofns',
type=int,
default=10,
help="Number of mock/random Fofns to write.")
U.add_fofn_output(p)
return p
def get_parser():
desc = "Transform pbreport Report to HTML file."
p = get_default_argparser(__version__, desc)
add_log_debug_option(p)
U.add_output_dir_option(p)
_add_report_option(p)
_add_output_file_option(p)
_add_ccs_js_extras_option(p)
p.set_defaults(func=_args_to_render_report)
return p
def add_run_show_templates_options(p):
#add_log_level_option(p)
add_log_debug_option(p)
def _to_h(m):
return "Resolve, Validate and Output Registered pipeline templates to {m} files to output-dir".format(
m=m)
p.add_argument('--output-templates-avro', type=str, help=_to_h("AVRO"))
p.add_argument('--output-templates-json', type=str, help=_to_h("JSON"))
p.add_argument('--show-all',
action="store_true",
help="Display developer/internal pipelines")
return p
def _get_argparser(level="INFO"):
p = argparse.ArgumentParser()
p.add_argument("--version", action="store_true")
add_log_level_option(add_log_debug_option(
add_log_quiet_option(add_log_verbose_option(p))),
default_level=level)
return p
def _get_argparser(level="INFO"):
p = argparse.ArgumentParser()
p.add_argument("--version", action="store_true")
add_log_level_option(
add_log_debug_option(add_log_quiet_option(add_log_verbose_option(p))), default_level=level
)
return p
def _add_run_random_fofn_options(p):
add_log_debug_option(p)
U.add_output_dir_option(p)
p.add_argument('--nfofns', type=int, default=10, help="Number of mock/random Fofns to write.")
U.add_fofn_output(p)
return p
def _add_base_options(p):
return _add_manifest_json_option(add_log_debug_option(p))
def add_args_run_diagnstic(p):
_add_required_preset_xml_option(p)
add_log_debug_option(p)
_add_output_dir_option(p)
_add_simple_mode_option(p)
return p
def _add_base_options(p):
return _add_manifest_json_option(add_log_debug_option(p))
def _add_run_dataset_report(p):
add_log_debug_option(p)
U.add_subread_input(p)
U.add_report_output(p)
return p
def add_args_run_diagnstic(p):
_add_required_preset_xml_option(p)
add_log_debug_option(p)
_add_output_dir_option(p)
_add_simple_mode_option(p)
return p
def _example_parser():
p = get_default_argparser("1.0.0", "Example Mock Parser")
p = CU.add_log_debug_option(p)
p.add_argument('example_file', type=str, help="No testing of existence")
return p
def _example_parser():
p = get_default_argparser("1.0.0", "Example Mock Parser")
p = CU.add_log_debug_option(p)
p.add_argument('example_file', type=str, help="No testing of existence")
return p
def _add_run_random_fastq_options(p):
add_log_debug_option(p)
p.add_argument('--max-records', type=int, default=1000, help="Max number of Fasta record to write.")
U.add_fastq_output(p)
return p
def _add_run_fasta_filter_options(p):
add_log_debug_option(p)
p.add_argument('--min-length', type=int, default=150, help='Min Length of Sequence to filter')
U.add_fasta_input(p)
U.add_fasta_output(p)
return p
def _add_run_dataset_report(p):
add_log_debug_option(p)
U.add_subread_input(p)
U.add_report_output(p)
return p
