def get_parser():
desc = "Tool to create Chunk json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help="Subparser Commands")
def builder(sid_, help_, opt_func_, exe_func_):
return U.subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
builder("fofn", "Create a generic chunk.json from a FOFN.", _add_chunk_fofn_options, _args_chunk_fofn)
builder("fasta", "Create a chunk.json from a Fasta file", _add_chunk_fasta_options, _args_run_chunk_fasta)
builder("fastq", "Create a chunk.json from a Fastq file", _add_chunk_fastq_options, _args_run_chunk_fastq)
builder("alignmentset",
"Create a chunk.json from an AlignmentSet XML file",
_add_chunk_alignmentset_options, _args_run_chunk_alignmentset)
builder("hdfsubreadset",
"Create a chunk.json from an HdfSubreadSet XML file",
_add_chunk_hdfsubreadset_options, _args_run_chunk_hdfsubreadset)
builder("subreadset",
"Create a chunk.json from an SubreadSet XML file",
_add_chunk_subreadset_options, _args_run_chunk_subreadset)
builder("csv", "Create a chunk.json CSV from a CSV file", _add_chunk_csv_options, _args_run_chunk_csv)
return p
def get_main_parser():
"""
Returns an argparse Parser with all the commandline utils as
subparsers
"""
desc = "General tool used by run task-manifests.json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help='Subparser Commands')
def builder(sid_, help_, opt_func_, exe_func_):
return U.subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
# Run command
builder('run', "Convert a Pacbio Input.xml file to Movie FOFN",
_add_run_options, _args_run_task_manifest)
builder("to-cmds", "Extract the cmds from manifest.json",
_add_manifest_json_option, _args_to_cmd)
builder(
"inspect",
"Pretty-Print a summary of the task-manifestExtract the cmds from manifest.json",
_add_base_options, _args_pprint_task_manifest)
return p
def get_main_parser():
p = get_default_argparser(
__version__, "Tool For generating MOCK data for development testing.")
sp = p.add_subparsers(help="Subparser Commands")
def _builder(subparser_id, desc, options_func, exe_func):
U.subparser_builder(sp, subparser_id, desc, options_func, exe_func)
_builder('fasta', "Generate a random Fasta file",
_add_run_random_fasta_file, _args_run_to_random_fasta_file)
_builder('fastq', "Generate a random Fastq File",
_add_run_random_fastq_options, _args_run_random_fastq_file)
_builder('fofn', "Generate a random FOFN file",
_add_run_random_fofn_options, _args_run_random_fofn)
_builder('filter-fasta', "Filter a Fasta file by sequence length",
_add_run_fasta_filter_options, _args_run_fasta_filter)
_builder("dataset-report", "DataSet Report Generator",
_add_run_dataset_report, _args_run_dataset_report)
_builder("reference-ds-report", "Reference DataSet Report Generator",
_add_run_reference_dataset_report,
_args_run_reference_dataset_report)
return p
def get_parser():
desc = "Tool to create Chunk json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help="Subparser Commands")
def builder(sid_, help_, opt_func_, exe_func_):
return U.subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
builder("fofn", "Create a generic chunk.json from a FOFN.",
_add_chunk_fofn_options, _args_chunk_fofn)
builder("fasta", "Create a chunk.json from a Fasta file",
_add_chunk_fasta_options, _args_run_chunk_fasta)
builder("fastq", "Create a chunk.json from a Fastq file",
_add_chunk_fastq_options, _args_run_chunk_fastq)
builder("alignmentset",
"Create a chunk.json from an AlignmentSet XML file",
_add_chunk_alignmentset_options, _args_run_chunk_alignmentset)
builder("hdfsubreadset",
"Create a chunk.json from an HdfSubreadSet XML file",
_add_chunk_hdfsubreadset_options, _args_run_chunk_hdfsubreadset)
builder("subreadset", "Create a chunk.json from an SubreadSet XML file",
_add_chunk_subreadset_options, _args_run_chunk_subreadset)
builder("csv", "Create a chunk.json CSV from a CSV file",
_add_chunk_csv_options, _args_run_chunk_csv)
return p
def get_parser():
desc = "Tool to import datasets, convert/import fasta file and run analysis jobs"
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help='commands')
def builder(subparser_id, description, options_func, exe_func):
subparser_builder(sp, subparser_id, description, options_func, exe_func)
status_desc = "Get System Status, DataSet and Job Summary"
builder('status', status_desc, add_base_and_sal_options, args_get_sal_summary)
local_desc = " The file location must be accessible from the host where the Services are running (often on a shared file system)"
ds_desc = "Import Local DataSet XML." + local_desc
builder('import-dataset', ds_desc, add_sal_and_xml_dir_options, args_runner_import_datasets)
fasta_desc = "Import Fasta (and convert to ReferenceSet)." + local_desc
builder("import-fasta", fasta_desc, add_import_fasta_opts, args_run_import_fasta)
run_analysis_desc = "Run Secondary Analysis Pipeline using an analysis.json"
builder("run-analysis", run_analysis_desc, add_run_analysis_job_opts, args_run_analysis_job)
emit_analysis_json_desc = "Emit an analysis.json Template to stdout that can be run using 'run-analysis'"
builder("emit-analysis-template", emit_analysis_json_desc, add_common_options, args_emit_analysis_template)
# Get Summary Job by Id
job_summary_desc = "Get Job Summary by Job Id"
builder('get-job', job_summary_desc, add_get_job_options, args_get_job_summary)
ds_summary_desc = "Get DataSet Summary by DataSet Id or UUID"
builder('get-dataset', ds_summary_desc, add_get_dataset_options, args_run_dataset_summary)
return p
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [
TU.add_debug_option, TU.add_override_chunked_mode,
TU.add_override_distribute_option
]
f = compose(*fs)
p = f(p)
p.add_argument(
'testkit_cfg_fofn',
type=validate_testkit_cfg_fofn,
help=
"File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg"
)
p.add_argument('-n',
'--nworkers',
type=int,
default=1,
help="Number of jobs to concurrently run.")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [
add_log_debug_option, TU.add_override_chunked_mode,
TU.add_override_distribute_option, add_ignore_test_failures_option
]
f = compose(*fs)
p = f(p)
p.add_argument(
'testkit_cfg_fofn',
type=validate_testkit_cfg_fofn,
help=
"File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg"
)
p.add_argument('-n',
'--nworkers',
type=int,
default=1,
help="Number of jobs to concurrently run.")
p.add_argument("-j",
"--junit-xml",
dest="junit_out",
action="store",
default="junit_combined_results.xml",
help="JUnit output file for all tests")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def get_main_parser():
desc = "Tool for testing current workflow configuration."
p = get_default_argparser(pbsmrtpipe.get_version(), desc)
_add_preset_xml_option(p)
_add_full_option(p)
p.set_defaults(func=_args_run_diagnostics)
return p
def get_main_parser():
desc = "Tool for testing current workflow configuration."
p = get_default_argparser(pbsmrtpipe.get_version(), desc)
_add_preset_xml_option(p)
_add_full_option(p)
p.set_defaults(func=_args_run_diagnostics)
return p
def get_parser():
p = get_default_argparser(__version__, __doc__)
p.add_argument("fasta_in", type=validate_file, help="Input Fasta")
p.add_argument("fasta_out", type=str, help="Output Fasta")
p.add_argument('--read-length', type=int, default=25, help="Min Sequence length to filter")
add_resolved_tool_contract_option(p)
# this parser cannot emit a tool contract, but can run from a resolved
# contract via --resolved-tool-contract /path/to/resolved-tool-contract.json
return p
def get_parser():
desc = "Gathering File Tool used within pbcoretools on chunk.json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help="Commands")
def builder(sid_, help_, opt_func_, exe_func_):
return subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
# CSV
builder('csv', "Merge CSV files into a single file.", _gather_csv_options,
_args_runner_gather_csv)
# Simple text
builder('txt', "Merge text files into a single file.", _gather_txt_options,
_args_runner_gather_txt)
# Fastq
builder('fastq', "Merge Fastq files into a single file.",
_gather_fastq_options, _args_runner_gather_fastq)
# Fasta
builder('fasta', "Merge Fasta files into a single file.",
_gather_fasta_options, _args_runner_gather_fasta)
builder('fofn', "Merge FOFNs into a single file.", _gather_fofn_options,
_args_runner_gather_fofn)
# Gff
builder('gff', "Merge Fasta files into a single file.",
_gather_gff_options, _args_runner_gather_gff)
# SubreadSet
builder('subreadset', "Merge SubreadSet XMLs into a single file.",
_gather_subreadset_options, _args_runner_gather_subreadset)
# AlignmentSet
builder('alignmentset', "Merge AlignmentSet XMLs into a single file.",
_gather_alignmentset_options, _args_runner_gather_alignmentset)
# ConsensusReadSet
builder('ccsset', "Merge ConsensusReadSet XMLs into a single file.",
_gather_ccsset_options, _args_runner_gather_ccsset)
# ConsensusAlignmentSet
builder('ccs_alignmentset',
"Merge ConsensusAlignmentSet XMLs into a single file.",
_gather_ccs_alignmentset_options,
_args_runner_gather_ccs_alignmentset)
# ContigSet
builder('contigset', "Merge ContigSet XMLs into a single file.",
_gather_contigset_options, _args_runner_gather_contigset)
return p
def get_parser():
desc = "Pbsmrtpipe workflow engine"
p = get_default_argparser(pbsmrtpipe.get_version(), desc)
sp = p.add_subparsers(help='commands')
def builder(subparser_id, description, options_func, exe_func):
TU.subparser_builder(sp, subparser_id, description, options_func,
exe_func)
wf_desc = "Run a pipeline using a pipeline template or with explict Bindings and EntryPoints."
builder('pipeline', wf_desc, add_pipline_parser_options,
_args_run_pipeline)
# Run a pipeline by id
pipline_id_desc = "Run a registered pipline by specifiying the pipline id."
builder('pipeline-id', pipline_id_desc, add_pipeline_id_parser_options,
_args_run_pipeline_id)
builder('task', "Run Task by id.", add_task_parser_options,
_args_task_runner)
# Show Templates
desc = "List all pipeline templates. A pipeline 'id' can be referenced in " \
"your my_pipeline.xml file using '<import-template id=\"pbsmrtpipe.pipelines.my_pipeline_id\" />. This " \
"can replace the explicit listing of EntryPoints and Bindings."
builder('show-templates', desc, add_run_show_templates_options,
_args_run_show_templates)
# Show Template Details
builder('show-template-details',
"Show details about a specific Pipeline template.",
add_show_template_details_parser_options,
_args_run_show_template_details)
# Show Tasks
show_tasks_desc = "Show completed list of Tasks by id. Use ENV {x} to define a " \
"custom directory of tool contracts. These TCs will override " \
"the installed TCs (e.g., {x}=/path/to/my-tc-dir/)".format(x=ENV_TC_DIR)
builder('show-tasks', show_tasks_desc, lambda x: x, _args_run_show_tasks)
# Show Task id details
desc_task_details = "Show Details of a particular task by id (e.g., 'pbsmrtpipe.tasks.filter_report'). Use 'show-tasks' to get a completed list of registered tasks."
builder('show-task-details', desc_task_details, add_show_task_options,
_args_run_show_task_details)
wfo_desc = "Display all workflow level options that can be set in <options /> for preset.xml"
builder('show-workflow-options', wfo_desc, _add_output_preset_xml_option,
_args_run_show_workflow_level_options)
diag_desc = "Diagnostic tests of preset.xml and cluster configuration"
builder('run-diagnostic', diag_desc, add_args_run_diagnstic,
_args_run_diagnostics)
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 get_parser():
desc = "Gathering File Tool used within pbcoretools on chunk.json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help="Commands")
def builder(sid_, help_, opt_func_, exe_func_):
return subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
# CSV
builder('csv', "Merge CSV files into a single file.",
_gather_csv_options, _args_runner_gather_csv)
# Simple text
builder('txt', "Merge text files into a single file.",
_gather_txt_options, _args_runner_gather_txt)
# Fastq
builder('fastq', "Merge Fastq files into a single file.",
_gather_fastq_options, _args_runner_gather_fastq)
# Fasta
builder('fasta', "Merge Fasta files into a single file.",
_gather_fasta_options, _args_runner_gather_fasta)
builder('fofn', "Merge FOFNs into a single file.",
_gather_fofn_options, _args_runner_gather_fofn)
# Gff
builder('gff', "Merge Fasta files into a single file.",
_gather_gff_options, _args_runner_gather_gff)
# SubreadSet
builder('subreadset', "Merge SubreadSet XMLs into a single file.",
_gather_subreadset_options, _args_runner_gather_subreadset)
# AlignmentSet
builder('alignmentset', "Merge AlignmentSet XMLs into a single file.",
_gather_alignmentset_options, _args_runner_gather_alignmentset)
# ConsensusReadSet
builder('ccsset', "Merge ConsensusReadSet XMLs into a single file.",
_gather_ccsset_options, _args_runner_gather_ccsset)
# ConsensusAlignmentSet
builder('ccs_alignmentset',
"Merge ConsensusAlignmentSet XMLs into a single file.",
_gather_ccs_alignmentset_options, _args_runner_gather_ccs_alignmentset)
# ContigSet
builder('contigset', "Merge ContigSet XMLs into a single file.",
_gather_contigset_options, _args_runner_gather_contigset)
return p
def get_parser():
p = get_default_argparser(__version__, __doc__)
p.add_argument("fasta_in", type=validate_file, help="Input Fasta")
p.add_argument("fasta_out", type=str, help="Output Fasta")
p.add_argument('--read-length',
type=int,
default=25,
help="Min Sequence length to filter")
add_resolved_tool_contract_option(p)
# this parser cannot emit a tool contract, but can run from a resolved
# contract via --resolved-tool-contract /path/to/resolved-tool-contract.json
return p
def _f(registry):
p = get_default_argparser(version, description)
sp = p.add_subparsers(help='Commands')
args_summary_runner = __args_summary_runner(registry)
args_rtc_runner = __args_rtc_runner(registry)
args_tc_emit = __args_emit_tc_runner(registry)
args_tcs_emit = __args_emit_all_tcs_runner(registry)
_subparser_builder(sp, Constants.RTC_DRIVER, "Run Resolved Tool contract", _add_run_rtc_options, args_rtc_runner)
_subparser_builder(sp, 'emit-tool-contracts', "Emit all Tool contracts to output-dir", _add_emit_all_tcs_options, args_tcs_emit)
_subparser_builder(sp, 'emit-tool-contract', "Emit a single tool contract by id", _add_emit_tc_options, args_tc_emit)
_subparser_builder(sp, 'summary', "Summary of Tool Contracts", lambda x: x, args_summary_runner)
return p
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser(__version__, desc)
funcs = [
TU.add_override_chunked_mode, TU.add_override_distribute_option,
_add_config_file_option, add_tests_only_option, add_log_level_option,
add_log_file_option, add_log_debug_option,
add_ignore_test_failures_option, add_output_xml_option
]
f = compose(*funcs)
p = f(p)
return p
def get_parser():
desc = "Pbsmrtpipe workflow engine"
p = get_default_argparser(pbsmrtpipe.get_version(), desc)
sp = p.add_subparsers(help='commands')
def builder(subparser_id, description, options_func, exe_func):
subparser_builder(sp, subparser_id, description, options_func, exe_func)
wf_desc = "Run a pipeline using a pipeline template or with explict Bindings and EntryPoints."
builder('pipeline', wf_desc, add_pipline_parser_options, _args_run_pipeline)
# Run a pipeline by id
pipline_id_desc = "Run a registered pipeline by specifying the pipeline id."
builder('pipeline-id', pipline_id_desc, add_pipeline_id_parser_options, _args_run_pipeline_id)
builder('task', "Run Task (i.e., ToolContract) by id", add_task_parser_options, _args_task_runner)
# Show Templates
desc = "List all pipeline templates. A pipeline 'id' can be referenced in " \
"your my_pipeline.xml file using '<import-template id=\"pbsmrtpipe.pipelines.my_pipeline_id\" />. This " \
"can replace the explicit listing of EntryPoints and Bindings."
builder('show-templates', desc, add_run_show_templates_options, _args_run_show_templates)
# Show Template Details
builder('show-template-details', "Show details about a specific Pipeline template.", add_show_template_details_parser_options, _args_run_show_template_details)
# Show Tasks
show_tasks_desc = "Show completed list of Tasks by id. Use ENV {x} to define a " \
"custom directory of tool contracts. These TCs will override " \
"the installed TCs (e.g., {x}=/path/to/my-tc-dir/)".format(x=ENV_TC_DIR)
builder('show-tasks', show_tasks_desc, lambda x: x, _args_run_show_tasks)
# Show Task id details
desc_task_details = "Show Details of a particular task by id (e.g., 'pbsmrtpipe.tasks.filter_report'). Use 'show-tasks' to get a completed list of registered tasks."
builder('show-task-details', desc_task_details, add_show_task_options, _args_run_show_task_details)
wfo_desc = "Display all workflow level options that can be set in <options /> for preset.xml"
builder('show-workflow-options', wfo_desc, _add_output_preset_xml_option, _args_run_show_workflow_level_options)
diag_desc = "Diagnostic tests of preset.xml and cluster configuration"
builder('run-diagnostic', diag_desc, add_args_run_diagnstic, _args_run_diagnostics)
desc_chunk_op_show = "Show a list of loaded chunk operators for Scatter/Gather Tasks. Extend resource loading by exporting ENV var {i}. Example export {i}=/path/to/chunk-operators-xml-dir".format(i=ENV_CHK_OPT_DIR)
builder('show-chunk-operators', desc_chunk_op_show, lambda x: x, _args_show_chunk_operator_summary)
return p
def get_parser():
desc = "Run multiple testkit.cfg files in parallel"
p = get_default_argparser(__version__, desc)
fs = [TU.add_debug_option,
TU.add_override_chunked_mode,
TU.add_override_distribute_option]
f = compose(*fs)
p = f(p)
p.add_argument('testkit_cfg_fofn', type=validate_testkit_cfg_fofn,
help="File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg")
p.add_argument('-n', '--nworkers', type=int, default=1, help="Number of jobs to concurrently run.")
p.set_defaults(func=_args_run_multi_testkit_cfg)
return p
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser(__version__, desc)
funcs = [TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_config_file_option,
add_tests_only_option,
add_log_level_option,
add_log_file_options,
TU.add_debug_option]
f = compose(*funcs)
p = f(p)
return p
def get_parser():
desc = "Tool to import datasets, convert/import fasta file and run analysis jobs"
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help="commands")
def builder(subparser_id, description, options_func, exe_func):
subparser_builder(sp, subparser_id, description, options_func, exe_func)
ds_desc = "Import DataSet XML "
builder("import-dataset", ds_desc, add_sal_and_xml_dir_options, args_runner_import_datasets)
rs_desc = "Import RS Metadata XML"
builder("import-rs-movie", rs_desc, add_sal_and_xml_dir_options, args_runner_import_rs_movies)
fasta_desc = "Import Fasta (and convert to ReferenceSet)"
builder("import-fasta", fasta_desc, add_import_fasta_opts, args_run_import_fasta)
return p
def get_main_parser():
p = get_default_argparser(__version__, "Tool For generating MOCK data for development testing.")
sp = p.add_subparsers(help="Subparser Commands")
def _builder(subparser_id, desc, options_func, exe_func):
U.subparser_builder(sp, subparser_id, desc, options_func, exe_func)
_builder('fasta', "Generate a random Fasta file", _add_run_random_fasta_file, _args_run_to_random_fasta_file)
_builder('fastq', "Generate a random Fastq File", _add_run_random_fastq_options, _args_run_random_fastq_file)
_builder('fofn', "Generate a random FOFN file", _add_run_random_fofn_options, _args_run_random_fofn)
_builder('filter-fasta', "Filter a Fasta file by sequence length", _add_run_fasta_filter_options, _args_run_fasta_filter)
_builder("dataset-report", "DataSet Report Generator", _add_run_dataset_report, _args_run_dataset_report)
_builder("reference-ds-report", "Reference DataSet Report Generator", _add_run_reference_dataset_report, _args_run_reference_dataset_report)
return p
def _f(registry):
p = get_default_argparser(version, description)
sp = p.add_subparsers(help='Commands')
args_summary_runner = __args_summary_runner(registry)
args_rtc_runner = __args_rtc_runner(registry)
args_tc_emit = __args_emit_tc_runner(registry)
args_tcs_emit = __args_emit_all_tcs_runner(registry)
_subparser_builder(sp, Constants.RTC_DRIVER,
"Run Resolved Tool contract", _add_run_rtc_options,
args_rtc_runner)
_subparser_builder(sp, 'emit-tool-contracts',
"Emit all Tool contracts to output-dir",
_add_emit_all_tcs_options, args_tcs_emit)
_subparser_builder(sp, 'emit-tool-contract',
"Emit a single tool contract by id",
_add_emit_tc_options, args_tc_emit)
_subparser_builder(sp, 'summary', "Summary of Tool Contracts",
lambda x: x, args_summary_runner)
return p
def get_main_parser():
"""
Returns an argparse Parser with all the commandline utils as
subparsers
"""
desc = "General tool used by run task-manifests.json files."
p = get_default_argparser(__version__, desc)
sp = p.add_subparsers(help='Subparser Commands')
def builder(sid_, help_, opt_func_, exe_func_):
return U.subparser_builder(sp, sid_, help_, opt_func_, exe_func_)
# Run command
builder('run', "Convert a Pacbio Input.xml file to Movie FOFN", _add_run_options, _args_run_task_manifest)
builder("to-cmds", "Extract the cmds from manifest.json", _add_manifest_json_option, _args_to_cmd)
builder("inspect", "Pretty-Print a summary of the task-manifestExtract the cmds from manifest.json",
_add_base_options, _args_pprint_task_manifest)
return p
def _example_parser():
p = get_default_argparser("1.0.0", "Example Mock Parser")
p = CU.add_debug_option(p)
p.add_argument('example_file', type=str, help="No testing of existence")
return p
def get_parser():
p = get_default_argparser("0.1.0", "Interactive tool for resolving Tool Contracts")
p.add_argument("tc_path", type=str, help='Path to Tool Contract')
p.set_defaults(func=_run_main)
return p
def get_parser():
desc = "Custom PipelineTemplate Registry to write pipeline templates to output directory"
p = get_default_argparser("0.1.0", desc)
p.add_argument('output_dir', help="Path to output directory")
return p
def get_parser():
desc = "Custom PipelineTemplate Registry to write pipeline templates to output directory"
p = get_default_argparser("0.1.0", desc)
p.add_argument('output_dir', help="Path to output directory")
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