diff env/lib/python3.9/site-packages/cwltool/argparser.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/cwltool/argparser.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,863 @@
+"""Command line argument parsing for cwltool."""
+
+import argparse
+import os
+from typing import (
+    Any,
+    AnyStr,
+    Dict,
+    List,
+    MutableMapping,
+    MutableSequence,
+    Optional,
+    Sequence,
+    Union,
+    cast,
+)
+
+from schema_salad.ref_resolver import file_uri
+
+from .loghandler import _logger
+from .process import Process, shortname
+from .resolver import ga4gh_tool_registries
+from .software_requirements import SOFTWARE_REQUIREMENTS_ENABLED
+from .utils import DEFAULT_TMP_PREFIX, onWindows
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        description="Reference executor for Common Workflow Language standards. "
+        "Not for production use."
+    )
+    parser.add_argument("--basedir", type=str)
+    parser.add_argument(
+        "--outdir",
+        type=str,
+        default=os.path.abspath("."),
+        help="Output directory. The default is the current directory.",
+    )
+
+    parser.add_argument(
+        "--parallel",
+        action="store_true",
+        default=False,
+        help="[experimental] Run jobs in parallel. ",
+    )
+    envgroup = parser.add_mutually_exclusive_group()
+    envgroup.add_argument(
+        "--preserve-environment",
+        type=str,
+        action="append",
+        help="Preserve specific environment variable when running "
+        "CommandLineTools without a software container.  May be provided "
+        "multiple times. The default is to preserve only the PATH.",
+        metavar="ENVVAR",
+        default=["PATH"],
+        dest="preserve_environment",
+    )
+    envgroup.add_argument(
+        "--preserve-entire-environment",
+        action="store_true",
+        help="Preserve all environment variables when running CommandLineTools "
+        "without a software container.",
+        default=False,
+        dest="preserve_entire_environment",
+    )
+
+    containergroup = parser.add_mutually_exclusive_group()
+    containergroup.add_argument(
+        "--rm-container",
+        action="store_true",
+        default=True,
+        help="Delete Docker container used by jobs after they exit (default)",
+        dest="rm_container",
+    )
+
+    containergroup.add_argument(
+        "--leave-container",
+        action="store_false",
+        default=True,
+        help="Do not delete Docker container used by jobs after they exit",
+        dest="rm_container",
+    )
+
+    cidgroup = parser.add_argument_group(
+        "Options for recording the Docker container identifier into a file."
+    )
+    cidgroup.add_argument(
+        # Disabled as containerid is now saved by default
+        "--record-container-id",
+        action="store_true",
+        default=False,
+        help=argparse.SUPPRESS,
+        dest="record_container_id",
+    )
+
+    cidgroup.add_argument(
+        "--cidfile-dir",
+        type=str,
+        help="Store the Docker container ID into a file in the specified directory.",
+        default=None,
+        dest="cidfile_dir",
+    )
+
+    cidgroup.add_argument(
+        "--cidfile-prefix",
+        type=str,
+        help="Specify a prefix to the container ID filename. "
+        "Final file name will be followed by a timestamp. "
+        "The default is no prefix.",
+        default=None,
+        dest="cidfile_prefix",
+    )
+
+    parser.add_argument(
+        "--tmpdir-prefix",
+        type=str,
+        help="Path prefix for temporary directories. If --tmpdir-prefix is not "
+        "provided, then the prefix for temporary directories is influenced by "
+        "the value of the TMPDIR, TEMP, or TMP environment variables. Taking "
+        "those into consideration, the current default is {}.".format(
+            DEFAULT_TMP_PREFIX
+        ),
+        default=DEFAULT_TMP_PREFIX,
+    )
+
+    intgroup = parser.add_mutually_exclusive_group()
+    intgroup.add_argument(
+        "--tmp-outdir-prefix",
+        type=str,
+        help="Path prefix for intermediate output directories. Defaults to the "
+        "value of --tmpdir-prefix.",
+        default="",
+    )
+
+    intgroup.add_argument(
+        "--cachedir",
+        type=str,
+        default="",
+        help="Directory to cache intermediate workflow outputs to avoid "
+        "recomputing steps. Can be very helpful in the development and "
+        "troubleshooting of CWL documents.",
+    )
+
+    tmpgroup = parser.add_mutually_exclusive_group()
+    tmpgroup.add_argument(
+        "--rm-tmpdir",
+        action="store_true",
+        default=True,
+        help="Delete intermediate temporary directories (default)",
+        dest="rm_tmpdir",
+    )
+
+    tmpgroup.add_argument(
+        "--leave-tmpdir",
+        action="store_false",
+        default=True,
+        help="Do not delete intermediate temporary directories",
+        dest="rm_tmpdir",
+    )
+
+    outgroup = parser.add_mutually_exclusive_group()
+    outgroup.add_argument(
+        "--move-outputs",
+        action="store_const",
+        const="move",
+        default="move",
+        help="Move output files to the workflow output directory and delete "
+        "intermediate output directories (default).",
+        dest="move_outputs",
+    )
+
+    outgroup.add_argument(
+        "--leave-outputs",
+        action="store_const",
+        const="leave",
+        default="move",
+        help="Leave output files in intermediate output directories.",
+        dest="move_outputs",
+    )
+
+    outgroup.add_argument(
+        "--copy-outputs",
+        action="store_const",
+        const="copy",
+        default="move",
+        help="Copy output files to the workflow output directory and don't "
+        "delete intermediate output directories.",
+        dest="move_outputs",
+    )
+
+    pullgroup = parser.add_mutually_exclusive_group()
+    pullgroup.add_argument(
+        "--enable-pull",
+        default=True,
+        action="store_true",
+        help="Try to pull Docker images",
+        dest="pull_image",
+    )
+
+    pullgroup.add_argument(
+        "--disable-pull",
+        default=True,
+        action="store_false",
+        help="Do not try to pull Docker images",
+        dest="pull_image",
+    )
+
+    parser.add_argument(
+        "--rdf-serializer",
+        help="Output RDF serialization format used by --print-rdf (one of "
+        "turtle (default), n3, nt, xml)",
+        default="turtle",
+    )
+
+    parser.add_argument(
+        "--eval-timeout",
+        help="Time to wait for a Javascript expression to evaluate before giving "
+        "an error, default 20s.",
+        type=float,
+        default=20,
+    )
+
+    provgroup = parser.add_argument_group(
+        "Options for recording provenance information of the execution"
+    )
+    provgroup.add_argument(
+        "--provenance",
+        help="Save provenance to specified folder as a "
+        "Research Object that captures and aggregates "
+        "workflow execution and data products.",
+        type=str,
+    )
+
+    provgroup.add_argument(
+        "--enable-user-provenance",
+        default=False,
+        action="store_true",
+        help="Record user account info as part of provenance.",
+        dest="user_provenance",
+    )
+    provgroup.add_argument(
+        "--disable-user-provenance",
+        default=False,
+        action="store_false",
+        help="Do not record user account info in provenance.",
+        dest="user_provenance",
+    )
+    provgroup.add_argument(
+        "--enable-host-provenance",
+        default=False,
+        action="store_true",
+        help="Record host info as part of provenance.",
+        dest="host_provenance",
+    )
+    provgroup.add_argument(
+        "--disable-host-provenance",
+        default=False,
+        action="store_false",
+        help="Do not record host info in provenance.",
+        dest="host_provenance",
+    )
+    provgroup.add_argument(
+        "--orcid",
+        help="Record user ORCID identifier as part of "
+        "provenance, e.g. https://orcid.org/0000-0002-1825-0097 "
+        "or 0000-0002-1825-0097. Alternatively the environment variable "
+        "ORCID may be set.",
+        dest="orcid",
+        default=os.environ.get("ORCID", ""),
+        type=str,
+    )
+    provgroup.add_argument(
+        "--full-name",
+        help="Record full name of user as part of provenance, "
+        "e.g. Josiah Carberry. You may need to use shell quotes to preserve "
+        "spaces. Alternatively the environment variable CWL_FULL_NAME may "
+        "be set.",
+        dest="cwl_full_name",
+        default=os.environ.get("CWL_FULL_NAME", ""),
+        type=str,
+    )
+
+    printgroup = parser.add_mutually_exclusive_group()
+    printgroup.add_argument(
+        "--print-rdf",
+        action="store_true",
+        help="Print corresponding RDF graph for workflow and exit",
+    )
+    printgroup.add_argument(
+        "--print-dot",
+        action="store_true",
+        help="Print workflow visualization in graphviz format and exit",
+    )
+    printgroup.add_argument(
+        "--print-pre",
+        action="store_true",
+        help="Print CWL document after preprocessing.",
+    )
+    printgroup.add_argument(
+        "--print-deps", action="store_true", help="Print CWL document dependencies."
+    )
+    printgroup.add_argument(
+        "--print-input-deps",
+        action="store_true",
+        help="Print input object document dependencies.",
+    )
+    printgroup.add_argument(
+        "--pack",
+        action="store_true",
+        help="Combine components into single document and print.",
+    )
+    printgroup.add_argument(
+        "--version", action="store_true", help="Print version and exit"
+    )
+    printgroup.add_argument(
+        "--validate", action="store_true", help="Validate CWL document only."
+    )
+    printgroup.add_argument(
+        "--print-supported-versions",
+        action="store_true",
+        help="Print supported CWL specs.",
+    )
+    printgroup.add_argument(
+        "--print-subgraph",
+        action="store_true",
+        help="Print workflow subgraph that will execute. Can combined with "
+        "--target or --single-step",
+    )
+    printgroup.add_argument(
+        "--print-targets", action="store_true", help="Print targets (output parameters)"
+    )
+    printgroup.add_argument(
+        "--make-template", action="store_true", help="Generate a template input object"
+    )
+
+    strictgroup = parser.add_mutually_exclusive_group()
+    strictgroup.add_argument(
+        "--strict",
+        action="store_true",
+        help="Strict validation (unrecognized or out of place fields are error)",
+        default=True,
+        dest="strict",
+    )
+    strictgroup.add_argument(
+        "--non-strict",
+        action="store_false",
+        help="Lenient validation (ignore unrecognized fields)",
+        default=True,
+        dest="strict",
+    )
+
+    parser.add_argument(
+        "--skip-schemas",
+        action="store_true",
+        help="Skip loading of schemas",
+        default=False,
+        dest="skip_schemas",
+    )
+
+    doccachegroup = parser.add_mutually_exclusive_group()
+    doccachegroup.add_argument(
+        "--no-doc-cache",
+        action="store_false",
+        help="Disable disk cache for documents loaded over HTTP",
+        default=True,
+        dest="doc_cache",
+    )
+    doccachegroup.add_argument(
+        "--doc-cache",
+        action="store_true",
+        help="Enable disk cache for documents loaded over HTTP",
+        default=True,
+        dest="doc_cache",
+    )
+
+    volumegroup = parser.add_mutually_exclusive_group()
+    volumegroup.add_argument("--verbose", action="store_true", help="Default logging")
+    volumegroup.add_argument(
+        "--quiet", action="store_true", help="Only print warnings and errors."
+    )
+    volumegroup.add_argument(
+        "--debug", action="store_true", help="Print even more logging"
+    )
+
+    parser.add_argument(
+        "--strict-memory-limit",
+        action="store_true",
+        help="When running with "
+        "software containers and the Docker engine, pass either the "
+        "calculated memory allocation from ResourceRequirements or the "
+        "default of 1 gigabyte to Docker's --memory option.",
+    )
+
+    parser.add_argument(
+        "--timestamps",
+        action="store_true",
+        help="Add timestamps to the errors, warnings, and notifications.",
+    )
+    parser.add_argument(
+        "--js-console", action="store_true", help="Enable javascript console output"
+    )
+    parser.add_argument(
+        "--disable-js-validation",
+        action="store_true",
+        help="Disable javascript validation.",
+    )
+    parser.add_argument(
+        "--js-hint-options-file",
+        type=str,
+        help="File of options to pass to jshint. "
+        'This includes the added option "includewarnings". ',
+    )
+    dockergroup = parser.add_mutually_exclusive_group()
+    dockergroup.add_argument(
+        "--user-space-docker-cmd",
+        metavar="CMD",
+        help="(Linux/OS X only) Specify the path to udocker. Implies --udocker",
+    )
+    dockergroup.add_argument(
+        "--udocker",
+        help="(Linux/OS X only) Use the udocker runtime for running containers "
+        "(equivalent to --user-space-docker-cmd=udocker).",
+        action="store_const",
+        const="udocker",
+        dest="user_space_docker_cmd",
+    )
+
+    dockergroup.add_argument(
+        "--singularity",
+        action="store_true",
+        default=False,
+        help="[experimental] Use "
+        "Singularity runtime for running containers. "
+        "Requires Singularity v2.6.1+ and Linux with kernel "
+        "version v3.18+ or with overlayfs support "
+        "backported.",
+    )
+    dockergroup.add_argument(
+        "--no-container",
+        action="store_false",
+        default=True,
+        help="Do not execute jobs in a "
+        "Docker container, even when `DockerRequirement` "
+        "is specified under `hints`.",
+        dest="use_container",
+    )
+
+    dependency_resolvers_configuration_help = argparse.SUPPRESS
+    dependencies_directory_help = argparse.SUPPRESS
+    use_biocontainers_help = argparse.SUPPRESS
+    conda_dependencies = argparse.SUPPRESS
+
+    if SOFTWARE_REQUIREMENTS_ENABLED:
+        dependency_resolvers_configuration_help = "Dependency resolver "
+        "configuration file describing how to adapt 'SoftwareRequirement' "
+        "packages to current system."
+        dependencies_directory_help = (
+            "Defaut root directory used by dependency resolvers configuration."
+        )
+        use_biocontainers_help = "Use biocontainers for tools without an "
+        "explicitly annotated Docker container."
+        conda_dependencies = (
+            "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
+        )
+
+    parser.add_argument(
+        "--beta-dependency-resolvers-configuration",
+        default=None,
+        help=dependency_resolvers_configuration_help,
+    )
+    parser.add_argument(
+        "--beta-dependencies-directory", default=None, help=dependencies_directory_help
+    )
+    parser.add_argument(
+        "--beta-use-biocontainers",
+        default=None,
+        help=use_biocontainers_help,
+        action="store_true",
+    )
+    parser.add_argument(
+        "--beta-conda-dependencies",
+        default=None,
+        help=conda_dependencies,
+        action="store_true",
+    )
+
+    parser.add_argument(
+        "--tool-help", action="store_true", help="Print command line help for tool"
+    )
+
+    parser.add_argument(
+        "--relative-deps",
+        choices=["primary", "cwd"],
+        default="primary",
+        help="When using --print-deps, print paths "
+        "relative to primary file or current working directory.",
+    )
+
+    parser.add_argument(
+        "--enable-dev",
+        action="store_true",
+        help="Enable loading and running unofficial development versions of "
+        "the CWL standards.",
+        default=False,
+    )
+
+    parser.add_argument(
+        "--enable-ext",
+        action="store_true",
+        help="Enable loading and running 'cwltool:' extensions to the CWL standards.",
+        default=False,
+    )
+
+    colorgroup = parser.add_mutually_exclusive_group()
+    colorgroup.add_argument(
+        "--enable-color",
+        action="store_true",
+        help="Enable logging color (default enabled)",
+        default=not onWindows(),
+    )
+    colorgroup.add_argument(
+        "--disable-color",
+        action="store_false",
+        dest="enable_color",
+        help="Disable colored logging (default false)",
+        default=onWindows(),
+    )
+
+    parser.add_argument(
+        "--default-container",
+        help="Specify a default software container to use for any "
+        "CommandLineTool without a DockerRequirement.",
+    )
+    parser.add_argument(
+        "--no-match-user",
+        action="store_true",
+        help="Disable passing the current uid to `docker run --user`",
+    )
+    parser.add_argument(
+        "--custom-net",
+        type=str,
+        help="Passed to `docker run` as the '--net' parameter when "
+        "NetworkAccess is true, which is its default setting.",
+    )
+    parser.add_argument(
+        "--disable-validate",
+        dest="do_validate",
+        action="store_false",
+        default=True,
+        help=argparse.SUPPRESS,
+    )
+
+    reggroup = parser.add_mutually_exclusive_group()
+    reggroup.add_argument(
+        "--enable-ga4gh-tool-registry",
+        action="store_true",
+        help="Enable tool resolution using GA4GH tool registry API",
+        dest="enable_ga4gh_tool_registry",
+        default=True,
+    )
+    reggroup.add_argument(
+        "--disable-ga4gh-tool-registry",
+        action="store_false",
+        help="Disable tool resolution using GA4GH tool registry API",
+        dest="enable_ga4gh_tool_registry",
+        default=True,
+    )
+
+    parser.add_argument(
+        "--add-ga4gh-tool-registry",
+        action="append",
+        help="Add a GA4GH tool registry endpoint to use for resolution, default %s"
+        % ga4gh_tool_registries,
+        dest="ga4gh_tool_registries",
+        default=[],
+    )
+
+    parser.add_argument(
+        "--on-error",
+        help="Desired workflow behavior when a step fails.  One of 'stop' (do "
+        "not submit any more steps) or 'continue' (may submit other steps that "
+        "are not downstream from the error). Default is 'stop'.",
+        default="stop",
+        choices=("stop", "continue"),
+    )
+
+    checkgroup = parser.add_mutually_exclusive_group()
+    checkgroup.add_argument(
+        "--compute-checksum",
+        action="store_true",
+        default=True,
+        help="Compute checksum of contents while collecting outputs",
+        dest="compute_checksum",
+    )
+    checkgroup.add_argument(
+        "--no-compute-checksum",
+        action="store_false",
+        help="Do not compute checksum of contents while collecting outputs",
+        dest="compute_checksum",
+    )
+
+    parser.add_argument(
+        "--relax-path-checks",
+        action="store_true",
+        default=False,
+        help="Relax requirements on path names to permit "
+        "spaces and hash characters.",
+        dest="relax_path_checks",
+    )
+
+    parser.add_argument(
+        "--force-docker-pull",
+        action="store_true",
+        default=False,
+        help="Pull latest software container image even if it is locally present",
+        dest="force_docker_pull",
+    )
+    parser.add_argument(
+        "--no-read-only",
+        action="store_true",
+        default=False,
+        help="Do not set root directory in the container as read-only",
+        dest="no_read_only",
+    )
+
+    parser.add_argument(
+        "--overrides",
+        type=str,
+        default=None,
+        help="Read process requirement overrides from file.",
+    )
+
+    subgroup = parser.add_mutually_exclusive_group()
+    subgroup.add_argument(
+        "--target",
+        "-t",
+        action="append",
+        help="Only execute steps that contribute to listed targets (can be "
+        "provided more than once).",
+    )
+    subgroup.add_argument(
+        "--single-step",
+        type=str,
+        default=None,
+        help="Only executes a single step in a workflow. The input object must "
+        "match that step's inputs. Can be combined with --print-subgraph.",
+    )
+
+    parser.add_argument(
+        "--mpi-config-file",
+        type=str,
+        default=None,
+        help="Platform specific configuration for MPI (parallel launcher, its "
+        "flag etc). See README section 'Running MPI-based tools' for details "
+        "of the format.",
+    )
+
+    parser.add_argument(
+        "workflow",
+        type=str,
+        nargs="?",
+        default=None,
+        metavar="cwl_document",
+        help="path or URL to a CWL Workflow, "
+        "CommandLineTool, or ExpressionTool. If the `inputs_object` has a "
+        "`cwl:tool` field indicating the path or URL to the cwl_document, "
+        " then the `cwl_document` argument is optional.",
+    )
+    parser.add_argument(
+        "job_order",
+        nargs=argparse.REMAINDER,
+        metavar="inputs_object",
+        help="path or URL to a YAML or JSON "
+        "formatted description of the required input values for the given "
+        "`cwl_document`.",
+    )
+
+    return parser
+
+
+def get_default_args() -> Dict[str, Any]:
+    """Get default values of cwltool's command line options."""
+    ap = arg_parser()
+    args = ap.parse_args([])
+    return vars(args)
+
+
+class FSAction(argparse.Action):
+    objclass = None  # type: str
+
+    def __init__(
+        self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
+    ) -> None:
+        """Fail if nargs is used."""
+        if nargs is not None:
+            raise ValueError("nargs not allowed")
+        super().__init__(option_strings, dest, **kwargs)
+
+    def __call__(
+        self,
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: Union[AnyStr, Sequence[Any], None],
+        option_string: Optional[str] = None,
+    ) -> None:
+        setattr(
+            namespace,
+            self.dest,
+            {
+                "class": self.objclass,
+                "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
+            },
+        )
+
+
+class FSAppendAction(argparse.Action):
+    objclass = None  # type: str
+
+    def __init__(
+        self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
+    ) -> None:
+        """Initialize."""
+        if nargs is not None:
+            raise ValueError("nargs not allowed")
+        super().__init__(option_strings, dest, **kwargs)
+
+    def __call__(
+        self,
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: Union[AnyStr, Sequence[Any], None],
+        option_string: Optional[str] = None,
+    ) -> None:
+        g = getattr(namespace, self.dest)
+        if not g:
+            g = []
+            setattr(namespace, self.dest, g)
+        g.append(
+            {
+                "class": self.objclass,
+                "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
+            }
+        )
+
+
+class FileAction(FSAction):
+    objclass = "File"
+
+
+class DirectoryAction(FSAction):
+    objclass = "Directory"
+
+
+class FileAppendAction(FSAppendAction):
+    objclass = "File"
+
+
+class DirectoryAppendAction(FSAppendAction):
+    objclass = "Directory"
+
+
+def add_argument(
+    toolparser: argparse.ArgumentParser,
+    name: str,
+    inptype: Any,
+    records: List[str],
+    description: str = "",
+    default: Any = None,
+    input_required: bool = True,
+) -> None:
+    if len(name) == 1:
+        flag = "-"
+    else:
+        flag = "--"
+
+    # if input_required is false, don't make the command line
+    # parameter required.
+    required = default is None and input_required
+    if isinstance(inptype, MutableSequence):
+        if inptype[0] == "null":
+            required = False
+            if len(inptype) == 2:
+                inptype = inptype[1]
+            else:
+                _logger.debug("Can't make command line argument from %s", inptype)
+                return None
+
+    ahelp = description.replace("%", "%%")
+    action = None  # type: Optional[Union[argparse.Action, str]]
+    atype = None  # type: Any
+
+    if inptype == "File":
+        action = cast(argparse.Action, FileAction)
+    elif inptype == "Directory":
+        action = cast(argparse.Action, DirectoryAction)
+    elif isinstance(inptype, MutableMapping) and inptype["type"] == "array":
+        if inptype["items"] == "File":
+            action = cast(argparse.Action, FileAppendAction)
+        elif inptype["items"] == "Directory":
+            action = cast(argparse.Action, DirectoryAppendAction)
+        else:
+            action = "append"
+    elif isinstance(inptype, MutableMapping) and inptype["type"] == "enum":
+        atype = str
+    elif isinstance(inptype, MutableMapping) and inptype["type"] == "record":
+        records.append(name)
+        for field in inptype["fields"]:
+            fieldname = name + "." + shortname(field["name"])
+            fieldtype = field["type"]
+            fielddescription = field.get("doc", "")
+            add_argument(toolparser, fieldname, fieldtype, records, fielddescription)
+        return
+    elif inptype == "string":
+        atype = str
+    elif inptype == "int":
+        atype = int
+    elif inptype == "double":
+        atype = float
+    elif inptype == "float":
+        atype = float
+    elif inptype == "boolean":
+        action = "store_true"
+    else:
+        _logger.debug("Can't make command line argument from %s", inptype)
+        return None
+
+    if inptype != "boolean":
+        typekw = {"type": atype}
+    else:
+        typekw = {}
+
+    toolparser.add_argument(
+        flag + name,
+        required=required,
+        help=ahelp,
+        action=action,  # type: ignore
+        default=default,
+        **typekw
+    )
+
+
+def generate_parser(
+    toolparser: argparse.ArgumentParser,
+    tool: Process,
+    namemap: Dict[str, str],
+    records: List[str],
+    input_required: bool = True,
+) -> argparse.ArgumentParser:
+    toolparser.description = tool.tool.get("doc", None)
+    toolparser.add_argument("job_order", nargs="?", help="Job input json file")
+    namemap["job_order"] = "job_order"
+
+    for inp in tool.tool["inputs"]:
+        name = shortname(inp["id"])
+        namemap[name.replace("-", "_")] = name
+        inptype = inp["type"]
+        description = inp.get("doc", "")
+        default = inp.get("default", None)
+        add_argument(
+            toolparser, name, inptype, records, description, default, input_required
+        )
+
+    return toolparser