diff env/lib/python3.7/site-packages/ephemeris/shed_tools_args.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/ephemeris/shed_tools_args.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,236 +0,0 @@
-"""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="[e-mail]",
-        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