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 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_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 _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 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 _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