--- a/env/lib/python3.7/site-packages/planemo/options.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1884 +0,0 @@
-"""Click definitions for various shared options and arguments."""
-
-from __future__ import absolute_import
-
-import functools
-import os
-
-import click
-from galaxy.tool_util.deps import docker_util
-
-from .config import planemo_option
-
-
-def force_option(what="files"):
-    return planemo_option(
-        "-f",
-        "--force",
-        is_flag=True,
-        help="Overwrite existing %s if present." % what,
-    )
-
-
-def skip_venv_option():
-    return planemo_option(
-        "--skip_venv",
-        is_flag=True,
-        help=("Do not create or source a virtualenv environment for Galaxy, "
-              "this should be used or instance to preserve an externally "
-              "configured virtual environment or conda environment.")
-    )
-
-
-def run_engine_option():
-    return planemo_option(
-        "--engine",
-        type=click.Choice(["galaxy", "docker_galaxy", "cwltool", "toil", "external_galaxy"]),
-        default=None,
-        use_global_config=True,
-        help=("Select an engine to run or test artifacts such as tools "
-              "and workflows. Defaults to a local Galaxy, but running Galaxy within "
-              "a Docker container or the CWL reference implementation 'cwltool' and "
-              "'toil' be selected.")
-    )
-
-
-def non_strict_cwl_option():
-    return planemo_option(
-        "--non_strict_cwl",
-        default=False,
-        is_flag=True,
-        help="Disable strict validation of CWL.",
-    )
-
-
-def serve_engine_option():
-    return planemo_option(
-        "--engine",
-        type=click.Choice(["galaxy", "docker_galaxy", "external_galaxy"]),
-        default="galaxy",
-        use_global_config=True,
-        use_env_var=True,
-        help=("Select an engine to serve artifacts such as tools "
-              "and workflows. Defaults to a local Galaxy, but running Galaxy within "
-              "a Docker container.")
-    )
-
-
-def ignore_dependency_problems_option():
-    return planemo_option(
-        "--ignore_dependency_problems",
-        is_flag=True,
-        default=False,
-        use_global_config=True,
-        help=("When installing shed repositories for workflows, ignore dependency issues. "
-              "These likely indicate a problem but in some cases may not prevent a workflow "
-              "from successfully executing.")
-    )
-
-
-def cwltool_no_container_option():
-    return planemo_option(
-        "--no-container",
-        "--no_container",
-        is_flag=True,
-        default=False,
-        use_global_config=True,
-        help=("If cwltool engine is used, disable Docker container usage.")
-    )
-
-
-def test_data_option():
-    return planemo_option(
-        "--test_data",
-        type=click.Path(exists=True, file_okay=False, resolve_path=True),
-        help="test-data directory to for specified tool(s).",
-    )
-
-
-def extra_tools_option():
-    return planemo_option(
-        "--extra_tools",
-        type=click.Path(exists=True,
-                        file_okay=True,
-                        dir_okay=True,
-                        resolve_path=True),
-        multiple=True,
-        help=("Extra tool sources to include in Galaxy's tool panel (file or "
-              "directory). These will not be linted/tested/etc... but they "
-              "will be available to workflows and for interactive use.")
-    )
-
-
-def tool_data_table_option():
-    return planemo_option(
-        "--tool_data_table",
-        type=click.Path(exists=True, file_okay=True, resolve_path=True),
-        help="tool_data_table_conf.xml file to for specified tool(s).",
-    )
-
-
-def galaxy_email_option():
-    return planemo_option(
-        "--galaxy_email",
-        type=str,
-        default="planemo@galaxyproject.org",
-        use_global_config=True,
-        use_env_var=True,
-        help="E-mail address to use when launching single-user Galaxy server.",
-    )
-
-
-def galaxy_python_version():
-    return planemo_option(
-        '--galaxy_python_version',
-        use_global_config=True,
-        default=None,
-        type=click.Choice(['2', '2.7', '3', '3.5', '3.6', '3.7', '3.8']),
-        help="Python version to start Galaxy under",
-    )
-
-
-def galaxy_root_option():
-    return planemo_option(
-        "--galaxy_root",
-        use_global_config=True,
-        extra_global_config_vars=["galaxy_root"],
-        use_env_var=True,
-        type=click.Path(file_okay=False, dir_okay=True, resolve_path=True),
-        help="Root of development galaxy directory to execute command with.",
-    )
-
-
-def galaxy_cwl_root_option():
-    return planemo_option(
-        "--cwl_galaxy_root",
-        use_global_config=True,
-        extra_global_config_vars=["cwl_galaxy_root"],
-        use_env_var=True,
-        type=click.Path(exists=True, file_okay=False, resolve_path=True),
-        help=("Root of development galaxy directory to execute command with"
-              " (must be branch of Galaxy with CWL support, this option"
-              " is experimental and will be replaced with --galaxy_root when"
-              " and if CWL support is merged into Galaxy."),
-    )
-
-
-def galaxy_port_option():
-    return planemo_option(
-        "--port",
-        type=int,
-        default="9090",
-        use_global_config=True,
-        help="Port to serve Galaxy on (default is 9090).",
-    )
-
-
-def galaxy_host_option():
-    return planemo_option(
-        "--host",
-        type=str,
-        default="127.0.0.1",
-        use_global_config=True,
-        help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
-              "restricted to localhost connections for security reasons "
-              "set to 0.0.0.0 to bind Galaxy to all ports including "
-              "potentially publicly accessible ones."),
-    )
-
-
-def dependency_resolvers_option():
-    return planemo_option(
-        "--dependency_resolvers_config_file",
-        type=click.Path(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            resolve_path=True
-        ),
-        use_global_config=True,
-        help="Dependency resolver configuration for Galaxy to target.",
-    )
-
-
-def enable_cwl_option():
-    return planemo_option(
-        "--cwl",
-        is_flag=True,
-        help=("Configure Galaxy for use with CWL tool."
-              " (this option is experimental and will be replaced when"
-              " and if CWL support is merged into Galaxy)."),
-    )
-
-
-def build_cwl_option():
-    return planemo_option(
-        "--cwl",
-        is_flag=True,
-        help="Build a CWL tool instead of a Galaxy tool.",
-    )
-
-
-def run_output_directory_option():
-    return planemo_option(
-        "output_directory",
-        "--output_directory",
-        "--outdir",
-        type=click.Path(
-            file_okay=False,
-            dir_okay=True,
-            resolve_path=True,
-        ),
-        default=None,
-        help=("Where to store outputs of a 'run' task."),
-    )
-
-
-def run_output_json_option():
-    return planemo_option(
-        "output_json",
-        "--output_json",
-        type=click.Path(
-            file_okay=True,
-            dir_okay=False,
-            resolve_path=True,
-        ),
-        default=None,
-        help=("Where to store JSON dictionary describing outputs of "
-              "a 'run' task."),
-    )
-
-
-def no_dependency_resolution():
-    return planemo_option(
-        "--no_dependency_resolution",
-        is_flag=True,
-        help="Configure Galaxy with no dependency resolvers.",
-    )
-
-
-def brew_dependency_resolution():
-    return planemo_option(
-        "--brew_dependency_resolution",
-        is_flag=True,
-        help="Configure Galaxy to use plain brew dependency resolution.",
-    )
-
-
-def conda_dependency_resolution():
-    return planemo_option(
-        "--conda_dependency_resolution",
-        is_flag=True,
-        help="Configure Galaxy to use only conda for dependency resolution.",
-    )
-
-
-def shed_dependency_resolution():
-    return planemo_option(
-        "--shed_dependency_resolution",
-        is_flag=True,
-        help=("Configure Galaxy to use brewed Tool Shed dependency"
-              " resolution."),
-    )
-
-
-def file_path_option():
-    return planemo_option(
-        "--file_path",
-        type=click.Path(
-            file_okay=False,
-            dir_okay=True,
-            resolve_path=True
-        ),
-        help="Location for files created by Galaxy (e.g. database/files).",
-        default=None,
-        use_global_config=True,
-    )
-
-
-def database_connection_option():
-    return planemo_option(
-        "--database_connection",
-        type=str,
-        help="Database connection string to use for Galaxy.",
-        default=None,
-        use_global_config=True,
-    )
-
-
-def shed_tools_conf_option():
-    return planemo_option(
-        "--shed_tool_conf",
-        type=str,
-        help="Location of shed tools conf file for Galaxy.",
-        default=None,
-        use_global_config=True,
-    )
-
-
-def shed_tools_directory_option():
-    return planemo_option(
-        "--shed_tool_path",
-        type=str,
-        help="Location of shed tools directory for Galaxy.",
-        default=None,
-        use_global_config=True,
-    )
-
-
-def tool_dependency_dir_option():
-    return planemo_option(
-        "--tool_dependency_dir",
-        type=click.Path(
-            exists=True,
-            file_okay=False,
-            dir_okay=True,
-            resolve_path=True
-        ),
-        default=None,
-        use_global_config=True,
-        help="Tool dependency dir for Galaxy to target.",
-    )
-
-
-def job_config_option():
-    return planemo_option(
-        "--job_config_file",
-        type=click.Path(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            resolve_path=True
-        ),
-        help="Job configuration file for Galaxy to target.",
-        default=None,
-        use_global_config=True,
-    )
-
-
-def mulled_containers_option():
-    return planemo_option(
-        "mulled_containers",
-        "--mulled_containers",
-        "--biocontainers",
-        is_flag=True,
-        help="Test tools against mulled containers (forces --docker).",
-    )
-
-
-def install_galaxy_option():
-    return planemo_option(
-        "--install_galaxy",
-        is_flag=True,
-        help="Download and configure a disposable copy of Galaxy from github."
-    )
-
-
-def docker_galaxy_image_option():
-    return planemo_option(
-        "--docker_galaxy_image",
-        default="quay.io/bgruening/galaxy",
-        use_global_config=True,
-        help=("Docker image identifier for docker-galaxy-flavor used if "
-              "engine type is specified as ``docker-galaxy``. Defaults to "
-              "quay.io/bgruening/galaxy.")
-    )
-
-
-def docker_extra_volume_option():
-    arg_type = click.Path(
-        exists=True,
-        file_okay=True,
-        dir_okay=True,
-        readable=True,
-        resolve_path=True,
-    )
-    return planemo_option(
-        "--docker_extra_volume",
-        type=arg_type,
-        default=None,
-        use_global_config=True,
-        help=("Extra path to mount if --engine docker.")
-    )
-
-
-def galaxy_url_option():
-    return planemo_option(
-        "--galaxy_url",
-        use_global_config=True,
-        extra_global_config_vars=["galaxy_url"],
-        use_env_var=True,
-        type=str,
-        help="Remote Galaxy URL to use with external Galaxy engine.",
-    )
-
-
-def galaxy_admin_key_option():
-    return planemo_option(
-        "--galaxy_admin_key",
-        use_global_config=True,
-        extra_global_config_vars=["admin_key"],
-        use_env_var=True,
-        type=str,
-        help="Admin key to use with external Galaxy engine.",
-    )
-
-
-def galaxy_user_key_option():
-    return planemo_option(
-        "--galaxy_user_key",
-        use_global_config=True,
-        extra_global_config_vars=["admin_key"],
-        use_env_var=True,
-        type=str,
-        help="User key to use with external Galaxy engine.",
-    )
-
-
-def no_cache_galaxy_option():
-    return planemo_option(
-        "--no_cache_galaxy",
-        is_flag=True,
-        help=("Skip caching of Galaxy source and dependencies obtained with "
-              "--install_galaxy. Not caching this results in faster "
-              "downloads (no git) - so is better on throw away instances such "
-              "with TravisCI. ")
-    )
-
-
-def galaxy_branch_option():
-    return planemo_option(
-        "--galaxy_branch",
-        default=None,
-        use_global_config=True,
-        use_env_var=True,
-        help=("Branch of Galaxy to target (defaults to master) if a Galaxy "
-              "root isn't specified.")
-    )
-
-
-def galaxy_source_option():
-    return planemo_option(
-        "--galaxy_source",
-        default=None,
-        use_global_config=True,
-        help=("Git source of Galaxy to target (defaults to the official "
-              "galaxyproject github source if a Galaxy root isn't "
-              "specified.")
-    )
-
-
-def skip_install_option():
-    return planemo_option(
-        "--skip_install",
-        is_flag=True,
-        help="Skip installation - only source requirements already available."
-    )
-
-
-def brew_option():
-    return planemo_option(
-        "--brew",
-        use_global_config=True,
-        type=click.Path(exists=True, file_okay=True, dir_okay=False),
-        help="Homebrew 'brew' executable to use."
-    )
-
-
-def conda_prefix_option():
-    return planemo_option(
-        "--conda_prefix",
-        use_global_config=True,
-        use_env_var=True,
-        type=click.Path(file_okay=False, dir_okay=True),
-        help="Conda prefix to use for conda dependency commands."
-    )
-
-
-def conda_exec_option():
-    return planemo_option(
-        "--conda_exec",
-        use_global_config=True,
-        type=click.Path(exists=True, file_okay=True, dir_okay=False),
-        help="Location of conda executable."
-    )
-
-
-def conda_debug_option():
-    return planemo_option(
-        "--conda_debug",
-        is_flag=True,
-        help="Enable more verbose conda logging."
-    )
-
-
-def conda_use_local_option():
-    return planemo_option(
-        "--conda_use_local",
-        is_flag=True,
-        help="Use locally built packages while building Conda environments."
-    )
-
-
-def conda_ensure_channels_option():
-    return planemo_option(
-        "conda_ensure_channels",
-        "--conda_channels",
-        "--conda_ensure_channels",
-        type=str,
-        use_global_config=True,
-        use_env_var=True,
-        help=("Ensure conda is configured with specified comma separated "
-              "list of channels."),
-        default="iuc,conda-forge,bioconda,defaults",
-    )
-
-
-def conda_copy_dependencies_option():
-    return planemo_option(
-        "--conda_copy_dependencies",
-        is_flag=True,
-        help=("Conda dependency resolution for Galaxy will copy dependencies "
-              "instead of attempting to link them.")
-    )
-
-
-def conda_auto_install_option():
-    return planemo_option(
-        "--conda_auto_install/--no_conda_auto_install",
-        is_flag=True,
-        default=True,
-        help=("Conda dependency resolution for Galaxy will attempt to install "
-              "requested but missing packages.")
-    )
-
-
-def conda_auto_init_option():
-    return planemo_option(
-        "--conda_auto_init/--no_conda_auto_init",
-        is_flag=True,
-        default=True,
-        help=("Conda dependency resolution for Galaxy will auto install "
-              "conda itself using miniconda if not availabe on conda_prefix.")
-    )
-
-
-def conda_global_option():
-    return planemo_option(
-        "--global",
-        is_flag=True,
-        default=False,
-        help=("Install Conda dependencies globally instead of in requirement specific "
-              "environments packaged for tools. If the Conda bin directory is on your "
-              "PATH, tools may still use binaries but this is more designed for "
-              "interactive testing and debugging.")
-    )
-
-
-def required_tool_arg(allow_uris=False):
-    """ Decorate click method as requiring the path to a single tool.
-    """
-    arg_type_class = click.Path if not allow_uris else UriLike
-    arg_type = arg_type_class(
-        exists=True,
-        file_okay=True,
-        dir_okay=False,
-        readable=True,
-        resolve_path=True,
-    )
-    if allow_uris:
-        name = "uri"
-        metavar = "TOOL_URI"
-    else:
-        name = "path"
-        metavar = "TOOL_PATH"
-    return click.argument(name, metavar=metavar, type=arg_type)
-
-
-def paste_test_data_paths_option():
-    return planemo_option(
-        "--paste_test_data_paths/--no_paste_test_data_paths",
-        is_flag=True,
-        default=None,
-        help=("By default Planemo will use or not use Galaxy's path paste option to load "
-              "test data into a history based on the engine type it is targeting. This can "
-              "override the logic to explicitly enable or disable path pasting.")
-    )
-
-
-def shed_install_option():
-    return planemo_option(
-        "--shed_install/--no_shed_install",
-        is_flag=True,
-        default=True,
-        help=("By default Planemo will attempt to install repositories needed for workflow "
-              "testing. This may not be appropriate for production servers and so this can "
-              "disabled by calling planemo with --no_shed_install.")
-    )
-
-
-def single_user_mode_option():
-    return planemo_option(
-        "galaxy_single_user",
-        "--galaxy_single_user/--no_galaxy_single_user",
-        is_flag=True,
-        default=True,
-        help=("By default Planemo will configure Galaxy to run in single-user mode where there "
-              "is just one user and this user is automatically logged it. Use --no_galaxy_single_user "
-              "to prevent Galaxy from running this way.")
-    )
-
-
-def required_workflow_arg():
-    arg_type = click.Path(
-        exists=True,
-        file_okay=True,
-        dir_okay=False,
-        readable=True,
-        resolve_path=False,
-    )
-    return click.argument("workflow_path", metavar="WORKFLOW_PATH", type=arg_type)
-
-
-def required_job_arg():
-    """Decorate click method as requiring the path to a single tool.
-    """
-    arg_type = click.Path(
-        exists=True,
-        file_okay=True,
-        dir_okay=False,
-        readable=True,
-        resolve_path=False,
-    )
-    return click.argument("job_path", metavar="JOB_PATH", type=arg_type)
-
-
-def _optional_tools_default(ctx, param, value):
-    if param.name in ["paths", "uris"] and len(value) == 0:
-        return [os.path.abspath(os.getcwd())]
-    else:
-        return value
-
-
-def optional_tools_or_packages_arg(multiple=False):
-    """ Decorate click method as optionally taking in the path to a tool
-    or directory of tools or a Conda package. If no such argument is given
-    the current working directory will be treated as a directory of tools.
-    """
-    name = "paths" if multiple else "path"
-    nargs = -1 if multiple else 1
-    return click.argument(
-        name,
-        metavar="TARGET",
-        nargs=nargs,
-    )
-
-
-class UriLike(click.Path):
-
-    def convert(self, value, param, ctx):
-        if "://" in value:
-            return value
-        else:
-            return super(UriLike, self).convert(value, param, ctx)
-
-
-def optional_tools_arg(multiple=False, allow_uris=False):
-    """ Decorate click method as optionally taking in the path to a tool
-    or directory of tools. If no such argument is given the current working
-    directory will be treated as a directory of tools.
-    """
-    arg_type_class = click.Path if not allow_uris else UriLike
-    arg_type = arg_type_class(
-        exists=True,
-        file_okay=True,
-        dir_okay=True,
-        readable=True,
-        resolve_path=True,
-    )
-    if allow_uris:
-        name = "uris" if multiple else "uri"
-    else:
-        name = "paths" if multiple else "path"
-    nargs = -1 if multiple else 1
-    return click.argument(
-        name,
-        metavar="TOOL_PATH",
-        type=arg_type,
-        nargs=nargs,
-        callback=_optional_tools_default,
-    )
-
-
-class ProjectOrRepositry(click.Path):
-
-    def __init__(self, **kwds):
-        super(ProjectOrRepositry, self).__init__(**kwds)
-
-    def convert(self, value, param, ctx):
-        if value and value.startswith("git:") or value.startswith("git+"):
-            return value
-        else:
-            return super(ProjectOrRepositry, self).convert(value, param, ctx)
-
-
-def shed_project_arg(multiple=True):
-    arg_type = ProjectOrRepositry(
-        exists=True,
-        file_okay=False,
-        dir_okay=True,
-        resolve_path=True,
-    )
-    name = "paths" if multiple else "path"
-    nargs = -1 if multiple else 1
-    return click.argument(
-        name,
-        metavar="PROJECT",
-        type=arg_type,
-        nargs=nargs,
-        callback=_optional_tools_default,
-    )
-
-
-def recipe_arg(multiple=True):
-    name = "paths" if multiple else "path"
-    nargs = -1 if multiple else 1
-    return click.argument(
-        name,
-        metavar="RECIPE_DIR",
-        type=click.Path(
-            exists=True,
-            file_okay=True,
-            dir_okay=True,
-            resolve_path=True,
-        ),
-        nargs=nargs,
-        callback=_optional_tools_default,
-    )
-
-
-def optional_project_arg(exists=True, default="."):
-    arg_type = click.Path(
-        exists=exists,
-        file_okay=False,
-        dir_okay=True,
-        writable=True,
-        resolve_path=True,
-    )
-    return click.argument(
-        "path",
-        metavar="PROJECT",
-        default=default,
-        type=arg_type
-    )
-
-
-def no_cleanup_option():
-    return planemo_option(
-        "--no_cleanup",
-        is_flag=True,
-        help=("Do not cleanup temp files created for and by Galaxy.")
-    )
-
-
-def docker_enable_option():
-    return planemo_option(
-        "--docker/--no_docker",
-        default=False,
-        help=("Run Galaxy tools in Docker if enabled.")
-    )
-
-
-def docker_cmd_option():
-    return planemo_option(
-        "--docker_cmd",
-        default=docker_util.DEFAULT_DOCKER_COMMAND,
-        help="Command used to launch docker (defaults to docker)."
-    )
-
-
-def docker_sudo_option():
-    return planemo_option(
-        "--docker_sudo/--no_docker_sudo",
-        is_flag=True,
-        help="Flag to use sudo when running docker."
-    )
-
-
-def docker_sudo_cmd_option():
-    return planemo_option(
-        "--docker_sudo_cmd",
-        help="sudo command to use when --docker_sudo is enabled " +
-             "(defaults to sudo).",
-        default=docker_util.DEFAULT_SUDO_COMMAND,
-        use_global_config=True,
-    )
-
-
-def docker_host_option():
-    return planemo_option(
-        "--docker_host",
-        help="Docker host to target when executing docker commands " +
-             "(defaults to localhost).",
-        use_global_config=True,
-        default=docker_util.DEFAULT_HOST,
-    )
-
-
-def docker_config_options():
-    return _compose(
-        docker_cmd_option(),
-        docker_sudo_option(),
-        docker_host_option(),
-        docker_sudo_cmd_option(),
-    )
-
-
-def galaxy_docker_options():
-    return _compose(
-        docker_enable_option(),
-        docker_config_options(),
-    )
-
-
-def shed_owner_option():
-    return planemo_option(
-        "--owner",
-        help="Tool Shed repository owner (username)."
-    )
-
-
-def shed_name_option():
-    return planemo_option(
-        "--name",
-        help="Tool Shed repository name (defaults to the inferred "
-             "tool directory name)."
-    )
-
-
-def validate_shed_target_callback(ctx, param, value):
-    if value is None:
-        ctx.fail("default_shed_target set to None, must specify a value for "
-                 "--shed_target to run this command.")
-    return value
-
-
-def shed_target_option():
-    return planemo_option(
-        "-t",
-        "--shed_target",
-        help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
-             "'local' (alias for http://localhost:9009/), an arbitrary url "
-             "or mappings defined ~/.planemo.yml.",
-        default=None,
-        use_global_config=True,
-        callback=validate_shed_target_callback,
-    )
-
-
-def shed_key_option():
-    return planemo_option(
-        "--shed_key",
-        help=("API key for Tool Shed access. An API key is required unless "
-              "e-mail and password is specified. This key can be specified "
-              "with either --shed_key or --shed_key_from_env.")
-    )
-
-
-def shed_key_from_env_option():
-    return planemo_option(
-        "--shed_key_from_env",
-        help="Environment variable to read API key for Tool Shed access from."
-    )
-
-
-def shed_email_option():
-    return planemo_option(
-        "--shed_email",
-        help="E-mail for Tool Shed auth (required unless shed_key is "
-             "specified)."
-    )
-
-
-def shed_password_option():
-    return planemo_option(
-        "--shed_password",
-        help="Password for Tool Shed auth (required unless shed_key is "
-             "specified)."
-    )
-
-
-def shed_skip_upload():
-    return planemo_option(
-        "--skip_upload",
-        is_flag=True,
-        help=("Skip upload contents as part of operation, only update "
-              "metadata.")
-    )
-
-
-def shed_skip_metadata():
-    return planemo_option(
-        "--skip_metadata",
-        is_flag=True,
-        help=("Skip metadata update as part of operation, only upload "
-              "new contents.")
-    )
-
-
-def shed_message_option():
-    return planemo_option(
-        "-m",
-        "--message",
-        help="Commit message for tool shed upload."
-    )
-
-
-def shed_force_create_option():
-    return planemo_option(
-        "--force_repository_creation",
-        help=("If a repository cannot be found for the specified user/repo "
-              "name pair, then automatically create the repository in the "
-              "toolshed."),
-        is_flag=True,
-        default=False
-    )
-
-
-def shed_check_diff_option():
-    return planemo_option(
-        "--check_diff",
-        is_flag=True,
-        help=("Skip uploading if the shed_diff detects there would be no "
-              "'difference' (only attributes populated by the shed would "
-              "be updated.)")
-    )
-
-
-def shed_upload_options():
-    return _compose(
-        shed_message_option(),
-        shed_force_create_option(),
-        shed_check_diff_option(),
-    )
-
-
-def shed_realization_options():
-    return _compose(
-        shed_project_arg(multiple=True),
-        recursive_shed_option(),
-        shed_fail_fast_option(),
-    )
-
-
-def shed_repo_options():
-    return _compose(
-        shed_owner_option(),
-        shed_name_option(),
-    )
-
-
-def shed_publish_options():
-    """ Common options for commands that require publishing to a
-    a shed.
-    """
-    return _compose(
-        shed_realization_options(),
-        shed_repo_options(),
-        shed_target_options(),
-    )
-
-
-def shed_read_options():
-    """ Common options that require read access to mapped repositories
-    in a shed.
-    """
-    return _compose(
-        shed_realization_options(),
-        shed_repo_options(),
-        shed_target_options(),
-    )
-
-
-def shed_target_options():
-    """ Common options for commands that require read-only
-    interactions with a shed.
-    """
-    return _compose(
-        shed_email_option(),
-        shed_key_option(),
-        shed_key_from_env_option(),
-        shed_password_option(),
-        shed_target_option(),
-    )
-
-
-def conda_target_options(include_local=True):
-    return _compose(
-        conda_prefix_option(),
-        conda_exec_option(),
-        conda_debug_option(),
-        conda_ensure_channels_option(),
-        conda_use_local_option(),
-    )
-
-
-def galaxy_run_options():
-    return _compose(
-        galaxy_target_options(),
-        galaxy_port_option(),
-        galaxy_host_option(),
-    )
-
-
-def galaxy_config_options():
-    return _compose(
-        test_data_option(),
-        tool_data_table_option(),
-        dependency_resolvers_option(),
-        brew_dependency_resolution(),
-        shed_dependency_resolution(),
-        no_dependency_resolution(),
-        conda_target_options(),
-        conda_dependency_resolution(),
-        conda_copy_dependencies_option(),
-        conda_auto_install_option(),
-        conda_auto_init_option(),
-        # Profile options...
-        profile_option(),
-        profile_database_options(),
-        file_path_option(),
-        database_connection_option(),
-        shed_tools_conf_option(),
-        shed_tools_directory_option(),
-        single_user_mode_option(),
-    )
-
-
-def galaxy_target_options():
-    return _compose(
-        galaxy_root_option(),
-        galaxy_python_version(),
-        extra_tools_option(),
-        install_galaxy_option(),
-        galaxy_branch_option(),
-        galaxy_source_option(),
-        skip_venv_option(),
-        no_cache_galaxy_option(),
-        no_cleanup_option(),
-        galaxy_email_option(),
-        galaxy_docker_options(),
-        mulled_containers_option(),
-        # Profile options...
-        job_config_option(),
-        tool_dependency_dir_option(),
-    )
-
-
-def pid_file_option():
-    pid_file_type = click.Path(
-        file_okay=True,
-        dir_okay=False,
-        resolve_path=True,
-    )
-    return planemo_option(
-        "--pid_file",
-        type=pid_file_type,
-        default=None,
-        help="Location of pid file is executed with --daemon."
-    )
-
-
-def daemon_option():
-    return planemo_option(
-        "--daemon",
-        is_flag=True,
-        help="Serve Galaxy process as a daemon."
-    )
-
-
-def profile_option():
-    return planemo_option(
-        "--profile",
-        type=str,
-        default=None,
-        help=("Name of profile (created with the profile_create command) to use "
-              "with this command.")
-    )
-
-
-def galaxy_serve_options():
-    return _compose(
-        galaxy_run_options(),
-        serve_engine_option(),
-        non_strict_cwl_option(),
-        docker_galaxy_image_option(),
-        docker_extra_volume_option(),
-        galaxy_config_options(),
-        daemon_option(),
-        pid_file_option(),
-        ignore_dependency_problems_option(),
-        shed_install_option()
-    )
-
-
-def training_topic_name_option():
-    return planemo_option(
-        "--topic_name",
-        required=True,
-        help="Name (directory name) of the topic to create or in which "
-             "a tutorial should be created or updates"
-    )
-
-
-def training_topic_option():
-    return _compose(
-        training_topic_name_option(),
-        planemo_option(
-            "--topic_title",
-            default="Title of the topic",
-            help="Title of the topic to create"),
-        planemo_option(
-            "--topic_summary",
-            default="Summary of the topic",
-            help="Summary of the topic"),
-        planemo_option(
-            "--topic_target",
-            type=click.Choice(['use', 'admin-dev', 'instructors']),
-            default="use",
-            help="Target audience for the topic")
-    )
-
-
-def training_tutorial_name_option():
-    return planemo_option(
-        "--tutorial_name",
-        help="Name (directory name) of the tutorial to create or to modify"
-    )
-
-
-def training_tutorial_name_req_option():
-    return planemo_option(
-        "--tutorial_name",
-        required=True,
-        help="Name (directory name) of the tutorial to modify"
-    )
-
-
-def training_datatype_option():
-    return planemo_option(
-        "--datatypes",
-        type=click.Path(file_okay=True, resolve_path=True),
-        help="YAML file with the correspondance between Zenodo extension and Galaxy datatypes",
-        default="shared/datatypes.yaml"
-    )
-
-
-def training_zenodo_option():
-    return planemo_option(
-        "--zenodo_link",
-        help="Zenodo URL with the input data")
-
-
-def training_tutorial_worflow_option():
-    return _compose(
-        planemo_option(
-            "--workflow",
-            type=click.Path(file_okay=True, resolve_path=True),
-            help="Workflow of the tutorial (locally)",
-            default=None),
-        planemo_option(
-            "--galaxy_url",
-            help="URL of a Galaxy instance with the workflow"),
-        planemo_option(
-            "--galaxy_api_key",
-            help="API key on the Galaxy instance with the workflow"),
-        planemo_option(
-            "--workflow_id",
-            help="ID of the workflow on the Galaxy instance")
-    )
-
-
-def training_tutorial_option():
-    return _compose(
-        training_tutorial_name_option(),
-        planemo_option(
-            "--tutorial_title",
-            default="Title of the tutorial",
-            help="Title of the tutorial"),
-        planemo_option(
-            "--hands_on",
-            is_flag=True,
-            default=True,
-            help="Add hands-on for the new tutorial"),
-        planemo_option(
-            "--slides",
-            is_flag=True,
-            default=False,
-            help="Add slides for the new tutorial"),
-        training_tutorial_worflow_option(),
-        training_zenodo_option()
-    )
-
-
-def training_init_options():
-    return _compose(
-        training_topic_option(),
-        training_tutorial_option(),
-        training_datatype_option()
-    )
-
-
-def training_fill_data_library_options():
-    return _compose(
-        training_topic_name_option(),
-        training_tutorial_name_req_option(),
-        training_zenodo_option(),
-        training_datatype_option()
-    )
-
-
-def training_generate_tuto_from_wf_options():
-    return _compose(
-        training_topic_name_option(),
-        training_tutorial_name_req_option(),
-        training_tutorial_worflow_option()
-    )
-
-
-def shed_fail_fast_option():
-    return planemo_option(
-        "--fail_fast",
-        is_flag=True,
-        default=False,
-        help="If multiple repositories are specified and an error occurs "
-             "stop immediately instead of processing remaining repositories."
-    )
-
-
-def lint_xsd_option():
-    return planemo_option(
-        "--xsd/--no_xsd",
-        is_flag=True,
-        default=True,
-        help=("Include tool XSD validation in linting process.")
-    )
-
-
-def report_level_option():
-    return planemo_option(
-        "--report_level",
-        type=click.Choice(["all", "warn", "error"]),
-        default="all",
-    )
-
-
-def report_xunit():
-    return planemo_option(
-        "--report_xunit",
-        type=click.Path(file_okay=True, resolve_path=True),
-        help="Output an XUnit report, useful for CI testing",
-        default=None,
-    )
-
-
-def skip_option():
-    return planemo_option(
-        "-s",
-        "--skip",
-        default=None,
-        help=("Comma-separated list of lint tests to skip (e.g. passing "
-              "--skip 'citations,xml_order' would skip linting of citations "
-              "and best-practice XML ordering.")
-    )
-
-
-def fail_level_option():
-    return planemo_option(
-        "--fail_level",
-        type=click.Choice(['warn', 'error']),
-        default="warn"
-    )
-
-
-def recursive_shed_option():
-    return recursive_option(
-        "Recursively perform command for nested repository directories.",
-    )
-
-
-def recursive_option(help="Recursively perform command for subdirectories."):
-    return planemo_option(
-        "-r",
-        "--recursive",
-        is_flag=True,
-        help=help,
-    )
-
-
-def merge_test_json():
-    target_path = click.Path(
-        file_okay=True,
-        dir_okay=False,
-        resolve_path=True,
-    )
-    return click.argument(
-        'input_paths',
-        metavar="INPUT_PATHS",
-        type=target_path,
-        nargs=-1,
-    )
-
-
-def tool_test_json(var="path"):
-    target_path = click.Path(
-        file_okay=True,
-        dir_okay=False,
-        resolve_path=True,
-    )
-    return click.argument(
-        var,
-        metavar="FILE_PATH",
-        type=target_path,
-        default="tool_test_output.json",
-    )
-
-
-def engine_options():
-    return _compose(
-        run_engine_option(),
-        non_strict_cwl_option(),
-        cwltool_no_container_option(),
-        docker_galaxy_image_option(),
-        docker_extra_volume_option(),
-        ignore_dependency_problems_option(),
-        shed_install_option(),
-        galaxy_url_option(),
-        galaxy_admin_key_option(),
-        galaxy_user_key_option(),
-    )
-
-
-def test_report_options():
-    return _compose(
-        planemo_option(
-            "--test_output",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            default="tool_test_output.html",
-            help=("Output test report (HTML - for humans) defaults to "
-                  "tool_test_output.html."),
-        ),
-        planemo_option(
-            "--test_output_text",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            help=("Output test report (Basic text - for display in CI)"),
-            default=None,
-        ),
-        planemo_option(
-            "--test_output_markdown",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            help=("Output test report (Markdown style - for humans & "
-                  "computers)"),
-            default=None,
-        ),
-        planemo_option(
-            "--test_output_xunit",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            help=("Output test report (xunit style - for CI systems"),
-            default=None,
-        ),
-        planemo_option(
-            "--test_output_junit",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            help=("Output test report (jUnit style - for CI systems"),
-            default=None,
-        ),
-    )
-
-
-def profile_name_argument():
-    return click.argument(
-        'profile_name',
-        metavar="PROFILE_NAME",
-        type=str,
-    )
-
-
-def database_identifier_argument():
-    return click.argument(
-        'identifier',
-        metavar="IDENTIFIER",
-        type=str,
-    )
-
-
-def postgres_datatype_type_option():
-    return planemo_option(
-        "--postgres",
-        "database_type",
-        flag_value="postgres",
-        help=("Use postgres database type."),
-    )
-
-
-def database_type_option():
-    return planemo_option(
-        "--database_type",
-        default="auto",
-        type=click.Choice([
-            "postgres",
-            "postgres_docker",
-            "sqlite",
-            "auto",
-        ]),
-        use_global_config=True,
-        help=("Type of database to use for profile - "
-              "'auto', 'sqlite', 'postgres', and 'postgres_docker' are available options. "
-              "Use postgres to use an existing postgres server you user can "
-              "access without a password via the psql command. Use postgres_docker "
-              "to have Planemo manage a docker container running postgres. "
-              "Data with postgres_docker is not yet persisted past when you restart "
-              "the docker container launched by Planemo so be careful with this option."),
-    )
-
-
-def database_source_options():
-    """Database connection options for commands that utilize a database."""
-    return _compose(
-        planemo_option(
-            "--postgres_psql_path",
-            default="psql",
-            use_global_config=True,
-            help=("Name or or path to postgres client binary (psql)."),
-        ),
-        planemo_option(
-            "--postgres_database_user",
-            default="postgres",
-            use_global_config=True,
-            help=("Postgres username for managed development databases."),
-        ),
-        planemo_option(
-            "--postgres_database_host",
-            default=None,
-            use_global_config=True,
-            help=("Postgres host name for managed development databases."),
-        ),
-        planemo_option(
-            "--postgres_database_port",
-            default=None,
-            use_global_config=True,
-            help=("Postgres port for managed development databases."),
-        ),
-    )
-
-
-def profile_database_options():
-    return _compose(
-        postgres_datatype_type_option(),
-        database_type_option(),
-        database_source_options(),
-    )
-
-
-def test_options():
-    return _compose(
-        planemo_option(
-            "--update_test_data",
-            is_flag=True,
-            help="Update test-data directory with job outputs (normally"
-                 " written to directory --job_output_files if specified.)"
-        ),
-        paste_test_data_paths_option(),
-        test_report_options(),
-        planemo_option(
-            "--test_output_json",
-            type=click.Path(file_okay=True, resolve_path=True),
-            use_global_config=True,
-            help=("Output test report (planemo json) defaults to "
-                  "tool_test_output.json."),
-            default="tool_test_output.json",
-        ),
-        planemo_option(
-            "--job_output_files",
-            type=click.Path(file_okay=False, resolve_path=True),
-            help="Write job outputs to specified directory.",
-            default=None,
-        ),
-        planemo_option(
-            "--summary",
-            type=click.Choice(["none", "minimal", "compact"]),
-            default="minimal",
-            help=("Summary style printed to planemo's standard output (see "
-                  "output reports for more complete summary). Set to 'none' "
-                  "to disable completely.")
-        )
-    )
-
-
-def _compose(*functions):
-    def compose2(f, g):
-        return lambda x: f(g(x))
-    return functools.reduce(compose2, functions)
-
-
-def dependencies_script_options():
-    return _compose(
-        planemo_option(
-            "--download_cache",
-            type=click.Path(file_okay=False, resolve_path=True),
-            use_global_config=True,
-            help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
-            default=None,
-        ),
-    )
-
-
-def filter_exclude_option():
-    return planemo_option(
-        "--exclude",
-        type=click.Path(resolve_path=False),
-        multiple=True,
-        help="Paths to exclude.",
-    )
-
-
-def filter_exclude_from_option():
-    return planemo_option(
-        "--exclude_from",
-        type=click.Path(exists=True, file_okay=True, dir_okay=False, resolve_path=True),
-        multiple=True,
-        help="File of paths to exclude.",
-    )
-
-
-def filter_changed_in_commit_option():
-    return planemo_option(
-        "--changed_in_commit_range",
-        help="Exclude paths unchanged in git commit range.",
-    )
-
-
-def ci_chunk_count_option():
-    return planemo_option(
-        "--chunk_count",
-        type=int,
-        help="Split output into chunks of this many item and print --chunk such group.",
-        default=1,
-    )
-
-
-def ci_chunk_option():
-    return planemo_option(
-        "--chunk",
-        type=int,
-        help=("When output is split into --chunk_count groups, output the group 0-indexed"
-              "by this option."),
-        default=0,
-    )
-
-
-def ci_output_option():
-    return planemo_option(
-        "--output",
-        help="File to output to, or - for standard output.",
-        default="-",
-    )
-
-
-def ci_find_options():
-    return _compose(
-        filter_exclude_option(),
-        filter_exclude_from_option(),
-        filter_changed_in_commit_option(),
-        ci_chunk_count_option(),
-        ci_chunk_option(),
-        ci_output_option(),
-    )
-
-
-def tool_init_id_option(prompt=True):
-    return planemo_option(
-        "-i",
-        "--id",
-        type=click.STRING,
-        prompt=prompt,
-        help="Short identifier for new tool (no whitespace)",
-    )
-
-
-def tool_init_tool_option():
-    return planemo_option(
-        "-t",
-        "--tool",
-        default=None,
-        type=click.Path(exists=False,
-                        file_okay=True,
-                        dir_okay=False,
-                        writable=True,
-                        resolve_path=True),
-        help="Output path for new tool (default is <id>.xml)",
-    )
-
-
-def tool_init_name_option(prompt=True, help="Name for new tool (user facing)"):
-    return planemo_option(
-        "-n",
-        "--name",
-        type=click.STRING,
-        prompt=prompt,
-        help=help,
-    )
-
-
-def tool_init_version_option():
-    return planemo_option(
-        "--version",
-        default="0.1.0",
-        type=click.STRING,
-        help="Tool XML version.",
-    )
-
-
-def tool_init_description_option():
-    return planemo_option(
-        "-d",
-        "--description",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help="Short description for new tool (user facing)",
-    )
-
-
-def tool_init_command_option():
-    return planemo_option(
-        "-c",
-        "--command",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help=("Command potentially including cheetah variables ()"
-              "(e.g. 'seqtk seq -a $input > $output')"),
-    )
-
-
-def tool_init_doi_option():
-    return planemo_option(
-        "--doi",
-        type=click.STRING,
-        default=None,
-        multiple=True,
-        prompt=False,
-        help=("Supply a DOI (http://www.doi.org/) easing citation of the tool "
-              "for Galxy users (e.g. 10.1101/014043).")
-    )
-
-
-def tool_init_test_case_option():
-    return planemo_option(
-        "--test_case",
-        is_flag=True,
-        default=None,
-        prompt=False,
-        help=("For use with --example_commmand, generate a tool test case from "
-              "the supplied example."),
-    )
-
-
-def tool_init_macros_option():
-    return planemo_option(
-        "--macros",
-        is_flag=True,
-        default=None,
-        prompt=False,
-        help="Generate a macros.xml for reuse across many tools.",
-    )
-
-
-def tool_init_cite_url_option():
-    return planemo_option(
-        "--cite_url",
-        type=click.STRING,
-        default=None,
-        multiple=True,
-        prompt=False,
-        help=("Supply a URL for citation.")
-    )
-
-
-def tool_init_input_option():
-    return planemo_option(
-        "--input",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        multiple=True,
-        help="An input description (e.g. input.fasta)",
-    )
-
-
-def tool_init_output_option():
-    return planemo_option(
-        "--output",
-        type=click.STRING,
-        multiple=True,
-        default=None,
-        prompt=False,
-        help=("An output location (e.g. output.bam), the Galaxy datatype is "
-              "inferred from the extension."),
-    )
-
-
-def tool_init_help_text_option():
-    return planemo_option(
-        "--help_text",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help="Help text (reStructuredText)",
-    )
-
-
-def tool_init_help_from_command_option():
-    return planemo_option(
-        "--help_from_command",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help="Auto populate help from supplied command.",
-    )
-
-
-def tool_init_example_input_option():
-    return planemo_option(
-        "--example_input",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        multiple=True,
-        help=("For use with --example_command, replace input file (e.g. 2.fastq "
-              "with a data input parameter)."),
-    )
-
-
-def tool_init_example_output_option():
-    return planemo_option(
-        "--example_output",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        multiple=True,
-        help=("For use with --example_command, replace input file (e.g. 2.fastq "
-              "with a tool output)."),
-    )
-
-
-def tool_init_named_output_option():
-    return planemo_option(
-        "--named_output",
-        type=click.STRING,
-        multiple=True,
-        default=None,
-        prompt=False,
-        help=("Create a named output for use with command block for example "
-              "specify --named_output=output1.bam and then use '-o $output1' "
-              "in your command block."),
-    )
-
-
-def tool_init_version_command_option():
-    return planemo_option(
-        "--version_command",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help="Command to print version (e.g. 'seqtk --version')",
-    )
-
-
-REQUIREMENT_HELP = "Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68')."
-
-
-def tool_init_requirement_option(help=REQUIREMENT_HELP):
-    return planemo_option(
-        "--requirement",
-        type=click.STRING,
-        default=None,
-        multiple=True,
-        prompt=False,
-        help=help,
-    )
-
-
-def tool_init_container_option():
-    return planemo_option(
-        "--container",
-        type=click.STRING,
-        default=None,
-        multiple=True,
-        prompt=False,
-        help="Add a Docker image identifier for this tool."
-    )
-
-
-EXAMPLE_COMMAND_HELP = (
-    "Example to command with paths to build Cheetah template from "
-    "(e.g. 'seqtk seq -a 2.fastq > 2.fasta'). Option cannot be used "
-    "with --command, should be used --example_input and "
-    "--example_output."
-)
-
-
-def tool_init_example_command_option(help=EXAMPLE_COMMAND_HELP):
-    return planemo_option(
-        "--example_command",
-        type=click.STRING,
-        default=None,
-        prompt=False,
-        help=help,
-    )
-
-
-def mulled_conda_option():
-    return planemo_option(
-        "--mulled_conda_version",
-        type=click.STRING,
-        default=None,
-        help=("Install a specific version of Conda before running the command, by "
-              "default the version that comes with the continuumio miniconda3 image "
-              "will be used under Linux and under Mac OS X Conda will be upgraded to "
-              "to work around a bug in 4.2.")
-    )
-
-
-def mulled_namespace_option():
-    return planemo_option(
-        "--mulled_namespace",
-        type=click.STRING,
-        default="biocontainers",
-        help=("Build a mulled image with the specified namespace - defaults to "
-              "biocontainers. Galaxy currently only recognizes images with the "
-              "namespace biocontainers.")
-    )
-
-
-def mulled_action_option():
-    return planemo_option(
-        "--mulled_command",
-        type=click.STRING,
-        default="build-and-test",
-        help=("Mulled action to perform for targets - this defaults to 'build-and-test'.")
-    )
-
-
-def mulled_options():
-    return _compose(
-        mulled_conda_option(),
-        mulled_namespace_option(),
-        mulled_action_option(),
-    )