--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo/lib/python3.7/site-packages/ephemeris/shed_tools_args.py	Fri Jul 31 00:18:57 2020 -0400
@@ -0,0 +1,236 @@
+"""This file contains the parser for shed_tools"""
+
+import argparse
+
+from .common_parser import get_common_args
+
+
+def parser():
+    """construct the parser object"""
+    common_arguments = get_common_args(log_file=True)
+    shed_parser = argparse.ArgumentParser()
+    subparsers = shed_parser.add_subparsers()
+
+    # A list of defaults is needed. Otherwise the shed-tools install parser will not return
+    # update_tools in the name space and shed-tool update will not return all the install
+    # variables.
+    shed_parser.set_defaults(
+        action="install",
+        tool_list_file=None,
+        tool_yaml=None,
+        owner=None,
+        name=None,
+        tool_panel_section_id=None,
+        tool_panel_section_label=None,
+        revisions=None,
+        tool_shed_url=None,
+        skip_tool_dependencies=False,
+        install_resolver_dependencies=False,
+        force_latest_revision=False,
+        test=False,
+        test_user_api_key=None,
+        test_user="ephemeris@galaxyproject.org",
+        test_json="tool_test_output.json",
+        test_existing=False,
+        parallel_tests=1,
+    )
+
+    # SUBPARSERS
+    install_command_parser = subparsers.add_parser(
+        "install",
+        help="This installs tools in Galaxy from the Tool Shed."
+             "Use shed-tools install --help for more information",
+        parents=[common_arguments],
+    )
+    update_command_parser = subparsers.add_parser(
+        "update",
+        help="This updates all tools in Galaxy to the latest revision. "
+             "Use shed-tools update --help for more information",
+        parents=[common_arguments])
+
+    test_command_parser = subparsers.add_parser(
+        "test",
+        help="This tests the supplied list of tools in Galaxy. "
+             "Use shed-tools test --help for more information",
+        parents=[common_arguments])
+
+    # SUBPARSER DEFAULTS
+    update_command_parser.set_defaults(
+        action="update"
+    )
+
+    test_command_parser.set_defaults(
+        action="test"
+    )
+    install_command_parser.set_defaults(
+        action="install"
+    )
+
+    # COMMON OPTIONS
+    for command_parser in [update_command_parser, install_command_parser, test_command_parser]:
+        command_parser.add_argument(
+            "-t", "--toolsfile",
+            dest="tool_list_file",
+            help="Tools file to use (see tool_list.yaml.sample)", )
+        command_parser.add_argument(
+            "-y", "--yaml_tool",
+            dest="tool_yaml",
+            help="Install tool represented by yaml string", )
+        command_parser.add_argument(
+            "--name",
+            help="The name of the tool to install (only applicable "
+                 "if the tools file is not provided).")
+        command_parser.add_argument(
+            "--owner",
+            help="The owner of the tool to install (only applicable "
+                 "if the tools file is not provided).")
+        command_parser.add_argument(
+            "--revisions",
+            default=None,
+            nargs='*',
+            dest="revisions",
+            help="The revisions of the tool repository that will be installed. "
+                 "All revisions must be specified after this flag by a space."
+                 "Example: --revisions 0a5c7992b1ac f048033da666"
+                 "(Only applicable if the tools file is not provided).")
+        command_parser.add_argument(
+            "--toolshed",
+            dest="tool_shed_url",
+            help="The Tool Shed URL where to install the tool from. "
+                 "This is applicable only if the tool info is "
+                 "provided as an option vs. in the tools file.")
+
+    # OPTIONS COMMON FOR UPDATE AND INSTALL
+
+    for command_parser in [update_command_parser, install_command_parser]:
+        command_parser.add_argument(
+            "--skip_install_tool_dependencies",
+            action="store_false",
+            dest="install_tool_dependencies",
+            default=False,  # Override True default for this function
+            help=argparse.SUPPRESS)  # Deprecated function. Leave for backwards compatibility.
+        command_parser.add_argument(
+            "--install_tool_dependencies",
+            action="store_true",
+            dest="install_tool_dependencies",
+            help="Turn on installation of tool dependencies using classic toolshed packages. "
+                 "Can be overwritten on a per-tool basis in the tools file.")
+        command_parser.add_argument(
+            "--install_resolver_dependencies",
+            action="store_true",
+            dest="install_resolver_dependencies",
+            default=True,  # Override False default for this function
+            help=argparse.SUPPRESS)  # Deprecated function. Leave for backwards compatibility.
+        command_parser.add_argument(
+            "--skip_install_resolver_dependencies",
+            action="store_false",
+            dest="install_resolver_dependencies",
+            help="Skip installing tool dependencies through resolver (e.g. conda). "
+                 "Will be ignored on galaxy releases older than 16.07. "
+                 "Can be overwritten on a per-tool basis in the tools file")
+        command_parser.add_argument(
+            "--skip_install_repository_dependencies",
+            action="store_false",
+            dest="install_repository_dependencies",
+            help="Skip installing the repository dependencies."
+        )
+        command_parser.add_argument(
+            "--test",
+            action="store_true",
+            dest="test",
+            help="Run tool tests on install tools, requires Galaxy 18.05 or newer."
+        )
+        command_parser.add_argument(
+            "--test_existing",
+            action="store_true",
+            help="If testing tools during install, also run tool tests on repositories already installed "
+                 "(i.e. skipped repositories)."
+        )
+        command_parser.add_argument(
+            "--test_json",
+            dest="test_json",
+            default="tool_test_output.json",
+            help="If testing tools, record tool test output to specified file. "
+                 "This file can be turned into reports with ``planemo test_reports <output.json>``."
+        )
+        command_parser.add_argument(
+            "--test_user_api_key",
+            dest="test_user",
+            help="If testing tools, a user is needed to execute the tests. "
+                 "This can be different the --api_key which is assumed to be an admin key. "
+                 "If --api_key is a valid user (e.g. it is not a master API key) this does "
+                 "not need to be specified and --api_key will be reused."
+        )
+        command_parser.add_argument(
+            "--test_user",
+            dest="test_user",
+            help="If testing tools, a user is needed to execute the tests. "
+                 "If --api_key is a master api key (i.e. not tied to a real user) and "
+                 "--test_user_api_key isn't specified, this user email will be used. This "
+                 "user will be created if needed."
+        )
+        command_parser.add_argument(
+            "--parallel_tests",
+            dest="parallel_tests",
+            default=1,
+            type=int,
+            help="Specify the maximum number of tests that will be run in parallel."
+        )
+
+    # OPTIONS UNIQUE TO INSTALL
+
+    install_command_parser.add_argument(
+        "--section",
+        dest="tool_panel_section_id",
+        help="Galaxy tool panel section ID where the tool will "
+             "be installed (the section must exist in Galaxy; "
+             "only applicable if the tools file is not provided).")
+    install_command_parser.add_argument(
+        "--section_label",
+        default=None,
+        dest="tool_panel_section_label",
+        help="Galaxy tool panel section label where tool will be installed "
+             "(if the section does not exist, it will be created; "
+             "only applicable if the tools file is not provided).")
+
+    install_command_parser.add_argument(
+        "--latest",
+        action="store_true",
+        dest="force_latest_revision",
+        help="Will override the revisions in the tools file and always install the latest revision.")
+
+    # OPTIONS UNIQUE TO TEST
+    # Same test_json as above but language modified for test instead of install/update.
+    test_command_parser.add_argument(
+        "--test_json",
+        default="tool_test_output.json",
+        dest="test_json",
+        help="Record tool test output to specified file. "
+             "This file can be turned into reports with ``planemo test_reports <output.json>``."
+    )
+
+    test_command_parser.add_argument(
+        "--test_user_api_key",
+        dest="test_user_api_key",
+        help="A user is needed to execute the tests. "
+             "This can be different the --api_key which is assumed to be an admin key. "
+             "If --api_key is a valid user (e.g. it is not a master API key) this does "
+             "not need to be specified and --api_key will be reused."
+    )
+    test_command_parser.add_argument(
+        "--test_user",
+        dest="test_user",
+        help="A user is needed to execute the tests. "
+             "If --api_key is a master api key (i.e. not tied to a real user) and "
+             "--test_user_api_key isn't specified, this user email will be used. This "
+             "user will be created if needed."
+    )
+    test_command_parser.add_argument(
+        "--parallel_tests",
+        dest="parallel_tests",
+        default=1,
+        type=int,
+        help="Specify the maximum number of tests that will be run in parallel."
+    )
+
+    return shed_parser