--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/planemo/options.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,1884 @@
+"""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(),
+    )