planemo package¶
Subpackages¶
- planemo.commands package
- Submodules
- planemo.commands.cmd_autoupdate module
- planemo.commands.cmd_ci_find_repos module
- planemo.commands.cmd_ci_find_tools module
- planemo.commands.cmd_ci_setup module
- planemo.commands.cmd_clone module
- planemo.commands.cmd_conda_build module
- planemo.commands.cmd_conda_env module
- planemo.commands.cmd_conda_init module
- planemo.commands.cmd_conda_install module
- planemo.commands.cmd_conda_search module
- planemo.commands.cmd_config_init module
- planemo.commands.cmd_container_register module
- planemo.commands.cmd_create_alias module
- planemo.commands.cmd_create_gist module
- planemo.commands.cmd_database_create module
- planemo.commands.cmd_database_delete module
- planemo.commands.cmd_database_list module
- planemo.commands.cmd_delete_alias module
- planemo.commands.cmd_docker_build module
- planemo.commands.cmd_docker_shell module
- planemo.commands.cmd_dockstore_init module
- planemo.commands.cmd_docs module
- planemo.commands.cmd_lint module
- planemo.commands.cmd_list_alias module
- planemo.commands.cmd_list_invocations module
- planemo.commands.cmd_list_repos module
- planemo.commands.cmd_merge_test_reports module
- planemo.commands.cmd_mull module
- planemo.commands.cmd_mulled_init module
- planemo.commands.cmd_normalize module
- planemo.commands.cmd_open module
- planemo.commands.cmd_profile_create module
- planemo.commands.cmd_profile_delete module
- planemo.commands.cmd_profile_list module
- planemo.commands.cmd_project_init module
- planemo.commands.cmd_pull_request module
- planemo.commands.cmd_rerun module
- planemo.commands.cmd_run module
- planemo.commands.cmd_serve module
- planemo.commands.cmd_share_test module
- planemo.commands.cmd_shed_build module
- planemo.commands.cmd_shed_create module
- planemo.commands.cmd_shed_diff module
- planemo.commands.cmd_shed_download module
- planemo.commands.cmd_shed_init module
- planemo.commands.cmd_shed_lint module
- planemo.commands.cmd_shed_serve module
- planemo.commands.cmd_shed_test module
- planemo.commands.cmd_shed_update module
- planemo.commands.cmd_shed_upload module
- planemo.commands.cmd_syntax module
- planemo.commands.cmd_test module
- planemo.commands.cmd_test_reports module
- planemo.commands.cmd_tool_init module
- planemo.commands.cmd_training_fill_data_library module
- planemo.commands.cmd_training_generate_from_wf module
- planemo.commands.cmd_training_init module
- planemo.commands.cmd_upload_data module
- planemo.commands.cmd_workflow_convert module
- planemo.commands.cmd_workflow_edit module
- planemo.commands.cmd_workflow_job_init module
- planemo.commands.cmd_workflow_lint module
- planemo.commands.cmd_workflow_test_init module
- planemo.commands.cmd_workflow_upload module
- Module contents
- planemo.cwl package
- planemo.database package
- planemo.engine package
- planemo.galaxy package
- Subpackages
- Submodules
- planemo.galaxy.activity module
- planemo.galaxy.api module
- planemo.galaxy.config module
- planemo.galaxy.distro_tools module
- planemo.galaxy.ephemeris_sleep module
- planemo.galaxy.profiles module
- planemo.galaxy.run module
- planemo.galaxy.serve module
- planemo.galaxy.workflows module
- Module contents
- planemo.linters package
- planemo.reports package
- planemo.shed package
- planemo.shed2tap package
- planemo.test package
- planemo.training package
- planemo.xml package
Submodules¶
planemo.autoupdate module¶
Autoupdate older conda dependencies in the requirements section.
-
planemo.autoupdate.
autoupdate_tool
(ctx: PlanemoCliContext, tool_path: str, modified_files: Set[Any], **kwds) → Optional[Set[str]][source]¶ Autoupdate an XML file
-
planemo.autoupdate.
autoupdate_wf
(ctx: PlanemoCliContext, config: LocalGalaxyConfig, wf: Runnable) → Dict[str, Any][source]¶
-
planemo.autoupdate.
check_conda
(package_name: str, ctx: PlanemoCliContext, **kwds) → str[source]¶ Get the most up-to-date conda version for a package.
-
planemo.autoupdate.
create_requirement_dict
(xml_files: Dict[str, xml.etree.ElementTree.ElementTree], skip_reqs: List[str]) → Tuple[Dict[str, Dict[str, Dict[str, Optional[str]]]], Optional[Tuple[str, str]]][source]¶ Create dict with requirements and find main requirement
-
planemo.autoupdate.
create_token_dict
(ctx: PlanemoCliContext, xml_files: Dict[str, xml.etree.ElementTree.ElementTree], main_req: Tuple[str, str], **kwds) → Tuple[Dict[str, Dict[str, Dict[str, Optional[str]]]], DefaultDict[str, List[Dict[str, str]]], Optional[str], Optional[str]][source]¶ Create dict with relevant tokens and check conda requirements for main
-
planemo.autoupdate.
find_macros
(xml_tree: xml.etree.ElementTree.ElementTree) → List[Any][source]¶ Get macros from the XML tree
-
planemo.autoupdate.
fix_workflow_ga
(original_wf: Dict[str, Any], updated_wf: Dict[str, Any]) → Dict[str, Any][source]¶
-
planemo.autoupdate.
fix_workflow_gxformat2
(original_wf: Dict[str, Any], updated_wf: Dict[str, Any]) → Dict[str, Any][source]¶
-
planemo.autoupdate.
get_requirements
(xml_tree: xml.etree.ElementTree.ElementTree) → Tuple[Dict[str, Dict[str, Optional[str]]], Optional[str]][source]¶ Get requirements from the XML tree
-
planemo.autoupdate.
get_tokens
(xml_tree: xml.etree.ElementTree.ElementTree) → Dict[str, Dict[str, Optional[str]]][source]¶ Get tokens from the XML tree
-
planemo.autoupdate.
get_tools_to_update
(ctx: PlanemoCliContext, workflow: Runnable, tools_to_skip: List[Any]) → Dict[str, Dict[str, str]][source]¶
-
planemo.autoupdate.
outdated_tools
(ctx: PlanemoCliContext, wf_dict: Dict[str, Any], ts: bioblend.toolshed.ToolShedInstance) → Dict[str, Dict[str, str]][source]¶
-
planemo.autoupdate.
perform_required_update
(ctx: PlanemoCliContext, xml_files: Dict[str, xml.etree.ElementTree.ElementTree], tool_path: str, requirements: Dict[str, Dict[str, Dict[str, Optional[str]]]], tokens: Dict[str, Dict[str, Dict[str, Optional[str]]]], xml_to_update: DefaultDict[str, List[Dict[str, str]]], wrapper_version_token: Union[str, int, None], **kwds) → Set[str][source]¶ Carry out the update, if requirements are out-of-date
planemo.ci module¶
Utilities for dealing with continous integration systems.
planemo.cli module¶
The module describes a CLI framework extending click
.
-
planemo.cli.
command_function
(f: Callable) → Callable[source]¶ Extension point for processing kwds after click callbacks.
-
planemo.cli.
name_to_command
(name: str) → click.core.Command[source]¶ Convert a subcommand name to the cli function for that command.
Command <X> is defined by the method ‘planemo.commands.cmd_<x>:cli’, this method uses __import__ to load and return that method.
-
class
planemo.cli.
PlanemoCliContext
[source]¶ Bases:
planemo.context.PlanemoContext
Describe context of Planemo CLI computation.
Extend PlanemoContext with operations for CLI concerns (exit code) and for interacting with the click library.
planemo.conda module¶
Planemo specific utilities for dealing with conda.
The extend galaxy-tool-util’s features with planemo specific idioms.
-
planemo.conda.
build_conda_context
(ctx: PlanemoCliContext, **kwds) → galaxy.tool_util.deps.conda_util.CondaContext[source]¶ Build a galaxy-tool-util CondaContext tailored to planemo use.
Using planemo’s common command-line/global config options.
-
planemo.conda.
collect_conda_targets
(ctx, paths, recursive=False, found_tool_callback=None)[source]¶ Load CondaTarget objects from supplied artifact sources.
If a tool contains more than one requirement, the requirements will each appear once in the output.
-
planemo.conda.
collect_conda_target_lists
(ctx, paths, recursive=False, found_tool_callback=None)[source]¶ Load CondaTarget lists from supplied artifact sources.
If a tool contains more than one requirement, the requirements will all appear together as one list element of the output list.
-
planemo.conda.
collect_conda_target_lists_and_tool_paths
(ctx, paths, recursive=False, found_tool_callback=None)[source]¶ Load CondaTarget lists from supplied artifact sources.
If a tool contains more than one requirement, the requirements will all appear together as one list element of the output list.
planemo.config module¶
Module defines abstractions for configuring Planemo.
-
planemo.config.
planemo_option
(*args, **kwargs) → Callable[source]¶ Extend
click.option
with planemo-config aware configuration.This extends click.option to use a callback when assigning default values, add
use_global_config
keyword argument to allow reading defaults from ~/.planemo.yml, and tracks how parameters are specified using the Planemo Context object.
planemo.context module¶
Define the context around Planemo computation.
Abstractions for cross cutting concerns (logging, workspace management, etc.).
-
planemo.context.
configure_standard_planemo_logging
(verbose: bool) → None[source]¶ Configure Planemo’s default logging rules.
-
class
planemo.context.
PlanemoContextInterface
[source]¶ Bases:
object
Interface Planemo operations use to access workspace context.
-
galaxy_profiles_directory
¶ Create a return a directory for storing Galaxy profiles.
-
global_config
¶ Read Planemo’s global configuration.
-
workspace
¶ Create and return Planemo’s workspace.
-
-
class
planemo.context.
PlanemoContext
[source]¶ Bases:
planemo.context.PlanemoContextInterface
Implementation of
PlanemoContextInterface
-
galaxy_profiles_directory
¶ Create a return a directory for storing Galaxy profiles.
-
get_option_source
(param_name: str) → OptionSource[source]¶ Return OptionSource value indicating how the option was set.
-
global_config
¶ Read Planemo’s global configuration.
As defined most simply by ~/.planemo.yml.
-
set_option_source
(param_name: str, option_source: OptionSource, force: bool = False) → None[source]¶ Specify how an option was set.
-
workspace
¶ Create and return Planemo’s workspace.
By default this will be
~/.planemo
.
-
planemo.deps module¶
Abstractions for building dependency resolution configurations.
planemo.docker module¶
Docker utilities for planemo.
Built on Galaxy abstractions in galaxy.tools.deps.dockerfiles
and
galaxy.tools.deps.docker_util
.
planemo.exit_codes module¶
Numeric constants for planemo exit codes.
planemo.git module¶
Utilities for interacting with git using planemo abstractions.
-
planemo.git.
checkout
(ctx, remote_repo, local_path, branch=None, remote='origin', from_branch='master')[source]¶ Checkout a new branch from a remote repository.
-
planemo.git.
clone
(*args, **kwds) → None[source]¶ Clone a git repository.
See
command_clone()
for description of arguments.
-
planemo.git.
command_clone
(ctx: PlanemoCliContext, src: str, dest: str, mirror: bool = False, branch: Optional[str] = None, depth: Optional[int] = None) → List[str][source]¶ Produce a command-line string to clone a repository.
Take in
ctx
to allow more configurability down the road.
-
planemo.git.
diff
(ctx: PlanemoCliContext, directory: str, range: str) → List[str][source]¶ Produce a list of diff-ed files for commit range.
-
planemo.git.
git_env_for
(path: str) → Dict[str, str][source]¶ Setup env dictionary to target specified git repo with git commands.
-
planemo.git.
is_rev_dirty
(ctx: PlanemoCliContext, directory: str) → bool[source]¶ Check if specified git repository has uncommitted changes.
-
planemo.git.
ls_remote
(ctx: PlanemoCliContext, remote_repo: str) → Dict[str, str][source]¶ Return a dictionary with refs as key and commits as value.
-
planemo.git.
push
(ctx: PlanemoCliContext, repo_path: str, to: Optional[str] = None, branch: Optional[str] = None, force: bool = False) → None[source]¶
planemo.github_util module¶
Utilities for interacting with Github.
-
planemo.github_util.
add_dir_contents_to_repo
(ctx, from_dir, target_dir, target_repository_path, version, dry_run, branch='main', notes='')[source]¶
-
planemo.github_util.
clone_fork_branch
(ctx, target, path, remote_name='planemo-remote', **kwds)[source]¶ Clone, fork, and branch a repository ahead of building a pull request.
-
planemo.github_util.
create_release
(ctx, from_dir, target_dir, owner, repo, version, dry_run, branch, notes='', **kwds)[source]¶
-
planemo.github_util.
ensure_gh
(ctx, **kwds)[source]¶ Ensure gh is available for planemo
This method will ensure
gh
is installed at the correct version.For more information on
gh
checkout https://cli.github.com/
-
planemo.github_util.
fork
(ctx, path, remote_name='planemo-remote', **kwds)[source]¶ Fork the target repository using
gh
.
-
planemo.github_util.
get_github_config
(ctx, allow_anonymous=False)[source]¶ Return a
planemo.github_util.GithubConfig
for given configuration.
-
planemo.github_util.
get_gh_env
(ctx, path=None, dry_run=False, **kwds)[source]¶ Return a environment dictionary to run gh with given user and repository target.
-
planemo.github_util.
get_or_create_repository
(ctx, owner, repo, dry_run=True, **kwds)[source]¶ Clones or creates a repository and returns path on disk
-
planemo.github_util.
publish_as_gist_file
(ctx, path, name='index')[source]¶ Publish a gist.
More information on gists at http://gist.github.com/.
planemo.io module¶
Planemo I/O abstractions and utilities.
-
planemo.io.
can_write_to_path
(path: str, **kwds)[source]¶ Implement -f/–force logic.
If supplied path exists, print an error message and return False unless –force caused the ‘force’ keyword argument to be True.
-
planemo.io.
captured_io_for_xunit
(kwds, captured_io)[source]¶ Capture Planemo I/O and timing for outputting to an xUnit report.
-
planemo.io.
communicate
(cmds, **kwds)[source]¶ Execute shell command and wait for output.
With click-aware I/O handling, pretty display of the command being executed, and formatted exception if the exit code is not 0.
-
planemo.io.
conditionally_captured_io
(capture, tee=False)[source]¶ If capture is True, capture stdout and stderr for logging.
-
planemo.io.
find_matching_directories
(path, pattern, recursive)[source]¶ Find directories below supplied path with file matching pattern.
Returns an empty list if no matches are found, and if recursive is False only the top directory specified by path will be considered.
-
planemo.io.
kill_pid_file
(pid_file: str)[source]¶ Kill process group corresponding to specified pid file.
-
planemo.io.
open_file_or_standard_output
(path, *args, **kwds)[source]¶ Open file but respect ‘-’ as referring to stdout.
-
planemo.io.
ps1_for_path
(path, base='PS1')[source]¶ Used by environment commands to build a PS1 shell variables for tool or directory of tools.
-
planemo.io.
real_io
()[source]¶ Ensure stdout and stderr have supported
fileno()
method.nosetests replaces these streams with
StringIO
objects that may not work the same in every situtation -subprocess.Popen()
calls in particular.
-
planemo.io.
tee_captured_output
(output)[source]¶ tee captured standard output and standard error if needed.
For messages captured with Capturing, send them to their correct locations so as to not interfere with normal user experience.
planemo.lint module¶
Utilities to help linting various targets.
-
planemo.lint.
build_lint_args
(ctx, **kwds)[source]¶ Handle common report, error, and skip linting arguments.
-
planemo.lint.
handle_lint_complete
(lint_ctx, lint_args, failed=False)[source]¶ Complete linting of a target and decide exit code.
-
planemo.lint.
lint_dois
(tool_xml, lint_ctx)[source]¶ Find referenced DOIs and check they have valid with https://doi.org.
planemo.mulled module¶
Planemo specific utilities for dealing with mulled containers.
The extend galaxy-tool-util’s features with planemo specific idioms.
-
planemo.mulled.
build_involucro_context
(ctx, **kwds)[source]¶ Build a galaxy-tool-util InvolucroContext tailored to planemo use.
Using planemo’s common command-line/global config options.
planemo.network_util module¶
planemo.options module¶
Click definitions for various shared options and arguments.
-
class
planemo.options.
ProjectOrRepositry
(**kwds)[source]¶ Bases:
click.types.Path
-
convert
(value, param, ctx)[source]¶ Convert the value to the correct type. This is not called if the value is
None
(the missing value).This must accept string values from the command line, as well as values that are already the correct type. It may also convert other compatible types.
The
param
andctx
arguments may beNone
in certain situations, such as when converting prompt input.If the value cannot be converted, call
fail()
with a descriptive message.Parameters: - value – The value to convert.
- param – The parameter that is using this type to convert
its value. May be
None
. - ctx – The current context that arrived at this value. May
be
None
.
-
-
class
planemo.options.
UriLike
(exists: bool = False, file_okay: bool = True, dir_okay: bool = True, writable: bool = False, readable: bool = True, resolve_path: bool = False, allow_dash: bool = False, path_type: Optional[Type[Any]] = None, executable: bool = False)[source]¶ Bases:
click.types.Path
-
convert
(value, param, ctx)[source]¶ Convert the value to the correct type. This is not called if the value is
None
(the missing value).This must accept string values from the command line, as well as values that are already the correct type. It may also convert other compatible types.
The
param
andctx
arguments may beNone
in certain situations, such as when converting prompt input.If the value cannot be converted, call
fail()
with a descriptive message.Parameters: - value – The value to convert.
- param – The parameter that is using this type to convert
its value. May be
None
. - ctx – The current context that arrived at this value. May
be
None
.
-
-
planemo.options.
cwltool_no_container_option
()[source]¶ Annotate click command as consume the –no_container option.
This option is for the CWL CLI runner interface.
-
planemo.options.
database_source_options
()[source]¶ Database connection options for commands that utilize a database.
-
planemo.options.
force_option
(what='files')[source]¶ Annotate click command as consume the -f/–force option.
-
planemo.options.
ignore_dependency_problems_option
()[source]¶ Annotate click command as consume the –ignore_dependency_problems option.
-
planemo.options.
non_strict_cwl_option
()[source]¶ Annotate click command as consume the –non_strict_cwl option.
-
planemo.options.
optional_tools_arg
(multiple=False, allow_uris=False)[source]¶ 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.
-
planemo.options.
optional_tools_or_packages_arg
(multiple=False)[source]¶ 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.
-
planemo.options.
required_job_arg
()[source]¶ Decorate click method as requiring the path to a single tool.
-
planemo.options.
required_tool_arg
(allow_uris=False)[source]¶ Decorate click method as requiring the path to a single tool.
-
planemo.options.
serve_engine_option
()[source]¶ Annotate click command as consume the –engine option.
This variant of the engine command is restricted to engines that can serve Galaxy servers.
-
planemo.options.
shed_publish_options
()[source]¶ Common options for commands that require publishing to a a shed.
-
planemo.options.
shed_read_options
()[source]¶ Common options that require read access to mapped repositories in a shed.
-
planemo.options.
shed_target_options
()[source]¶ Common options for commands that require read-only interactions with a shed.
-
planemo.options.
skip_client_build_option
()[source]¶ Annotate click command as consume the –skip_client_build option.
-
planemo.options.
skip_venv_option
()[source]¶ Annotate click command as consume the –skip_venv option.
-
planemo.options.
test_data_option
()[source]¶ Annotate click command as consume the –test_data option.
-
planemo.options.
tool_init_example_command_option
(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.")[source]¶
planemo.runnable module¶
Describe artifacts that can be run, tested, and linted.
-
planemo.runnable.
cases
(runnable: planemo.runnable.Runnable) → List[planemo.runnable.AbstractTestCase][source]¶ Build a list of
TestCase
objects for specified runnable.
-
class
planemo.runnable.
ErrorRunResponse
(error_message, job_info=None, invocation_details=None, log=None, start_datetime=None, end_datetime=None)[source]¶ Bases:
planemo.runnable.RunResponse
Description of an error while attempting to execute a Runnable.
-
end_datetime
¶ End datetime of run.
-
error_message
¶ Error message describing the problem with execution of the runnable.
-
invocation_details
¶ If workflow invocation details are available, return as dictionary.
-
job_info
¶ Return potentially null stored job_info dict.
-
log
¶ Return potentially null stored log text.
-
start_datetime
¶ Start datetime of run.
-
was_successful
¶ Return False to indicate this run was successful.
-
-
planemo.runnable.
for_path
(path: str) → Union[planemo.runnable.Runnable, List[planemo.runnable.Runnable]][source]¶ Produce a class:Runnable for supplied path.
-
planemo.runnable.
for_paths
(paths: Iterable[str]) → List[planemo.runnable.Runnable][source]¶ Return a specialized list of Runnable objects for paths.
-
planemo.runnable.
get_outputs
(runnable: planemo.runnable.Runnable, gi: Optional[bioblend.galaxy.GalaxyInstance] = None) → List[planemo.runnable.RunnableOutput][source]¶ Return a list of
RunnableOutput
objects for this runnable.Supply bioblend user Galaxy instance object (as gi) if additional context needed to resolve workflow details.
-
class
planemo.runnable.
Runnable
[source]¶ Bases:
tuple
Abstraction describing tools and workflows.
-
data_manager_conf_path
¶ Path of a Galaxy data manager configuration for runnable or None.
-
has_path
¶
-
has_tools
¶ Boolean indicating if this runnable corresponds to one or more tools.
-
is_remote_workflow_uri
¶
-
is_single_artifact
¶ Boolean indicating if this runnable is a single artifact.
Currently only directories are considered not a single artifact.
-
path
¶
-
test_data_search_path
¶ During testing, path to search for test data files.
-
tool_data_search_path
¶ During testing, path to search for Galaxy tool data tables.
-
type
¶ Alias for field number 1
-
uri
¶ Alias for field number 0
-
-
class
planemo.runnable.
RunnableType
[source]¶ Bases:
enum.Enum
An enumeration.
-
cwl_tool
= 4¶
-
cwl_workflow
= 5¶
-
directory
= 6¶
-
galaxy_datamanager
= 2¶
-
galaxy_tool
= 1¶
-
galaxy_workflow
= 3¶
-
has_tools
¶
-
is_cwl_artifact
¶
-
is_galaxy_artifact
¶
-
is_single_artifact
¶
-
test_data_in_parent_dir
¶
-
-
class
planemo.runnable.
RunResponse
[source]¶ Bases:
object
Description of an attempt for an engine to execute a Runnable.
-
end_datetime
¶ End datetime of run.
-
invocation_details
¶ If workflow invocation details are available, return as dictionary.
-
job_info
¶ If job information is available, return as dictionary.
-
log
¶ If engine related log is available, return as text data.
-
start_datetime
¶ Start datetime of run.
-
was_successful
¶ Indicate whether an error was encountered while executing this runnable.
If successful, response should conform to the SuccessfulRunResponse interface, otherwise it will conform to the ErrorRunResponse interface.
-
-
class
planemo.runnable.
RunnableOutput
[source]¶ Bases:
object
Description of a single output of an execution of a Runnable.
-
get_id
¶ An identifier that describes this output.
-
-
class
planemo.runnable.
SuccessfulRunResponse
(runnable: planemo.runnable.Runnable)[source]¶ Bases:
planemo.runnable.RunResponse
Description of the results of an engine executing a Runnable.
-
outputs_dict
¶ Return a dict of output descriptions.
-
was_successful
¶ Return True to indicate this run was successful.
-
-
class
planemo.runnable.
TestCase
(runnable: planemo.runnable.Runnable, tests_directory: str, output_expectations: Dict[str, Any], job_path: Optional[str], job: Optional[Dict[KT, VT]], index: int, doc: Optional[str])[source]¶ Bases:
planemo.runnable.AbstractTestCase
Describe an abstract test case for a specified runnable.
-
input_ids
¶ Labels of inputs specified in test description.
-
structured_test_data
(run_response: planemo.runnable.RunResponse) → Dict[str, Any][source]¶ Check a test case against outputs dictionary.
-
tested_output_ids
¶ Labels of outputs checked in test description.
-
planemo.runnable_resolve module¶
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planemo.runnable_resolve.
for_runnable_identifier
(ctx, runnable_identifier, kwds)[source]¶ Convert URI, path, or alias into Runnable.
planemo.shed_lint module¶
Logic related to linting shed repositories.
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planemo.shed_lint.
lint_repository
(ctx, realized_repository, **kwds)[source]¶ Lint a realized shed repository.
See
planemo.shed
for details on constructing a realized repository data structure.
planemo.templates module¶
Templating abstraction around jinja2 for Planemo.
planemo.tool_builder module¶
This module contains build()
to build tool descriptions.
This class is used by the tool_init command and can be used to build Galaxy and CWL tool descriptions.
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planemo.tool_builder.
build
(**kwds)[source]¶ Build up a
ToolDescription()
from supplid arguments.
planemo.tool_lint module¶
planemo.tools module¶
Planemo-specific wrappers around galaxy-tool-util tool functionality.
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planemo.tools.
is_tool_load_error
(obj)[source]¶ Predicate to determine if object loaded for tool is a tool error.
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planemo.tools.
load_tool_sources_from_path
(path: str, recursive: bool, register_load_errors: bool = False) → List[Tuple[str, Union[galaxy.tool_util.parser.interface.ToolSource, object]]][source]¶ Generate a list for tool sources found down specified path.
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planemo.tools.
yield_tool_sources
(ctx: Optional[PlanemoCliContext], path: str, recursive: bool = False, yield_load_errors: bool = True) → Iterator[Tuple[str, Union[galaxy.tool_util.parser.interface.ToolSource, object]]][source]¶ Walk single path and yield ToolSource objects discovered.
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planemo.tools.
yield_tool_sources_on_paths
(ctx: Optional[PlanemoCliContext], paths: Iterable[str], recursive: bool = False, yield_load_errors: bool = True, exclude_deprecated: bool = False) → Iterator[Tuple[str, Union[galaxy.tool_util.parser.interface.ToolSource, object]]][source]¶ Walk paths and yield ToolSource objects discovered.
planemo.virtualenv module¶
Utilities for using virtualenv as library and planemo command.
planemo.workflow_lint module¶
-
class
planemo.workflow_lint.
WorkflowLintContext
(level: Union[galaxy.tool_util.lint.LintLevel, str], lint_message_class: Type[galaxy.tool_util.lint.LintMessage] = <class 'galaxy.tool_util.lint.LintMessage'>, skip_types: Optional[List[str]] = None, object_name: Optional[str] = None)[source]¶ Bases:
galaxy.tool_util.lint.LintContext
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training_topic
= None¶
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planemo.workflow_lint.
find_potential_workflow_files
(directory: str) → List[str][source]¶ Return a list of potential workflow files in a directory.
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planemo.workflow_lint.
find_repos_from_tool_id
(tool_id: str, ts: bioblend.toolshed.ToolShedInstance) → Tuple[str, Dict[str, Any]][source]¶ Return a string which indicates what failed and dict with all revisions for a given tool id