guppy_basecaller: env/lib/python3.7/site-packages/planemo/options.py comparison

comparison env/lib/python3.7/site-packages/planemo/options.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

author	shellac
date	Sat, 02 May 2020 07:14:21 -0400
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:26e78fe6e8c4
+"""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(),
+)

Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/options.py @ 0:26e78fe6e8c4 draft