galaxy.tools package¶
Subpackages¶
- galaxy.tools.cwl package
- galaxy.tools.deps package
- Subpackages
- galaxy.tools.deps.container_resolvers package
- galaxy.tools.deps.mulled package
- Submodules
- galaxy.tools.deps.mulled.mulled_build module
- galaxy.tools.deps.mulled.mulled_build_channel module
- galaxy.tools.deps.mulled.mulled_build_files module
- galaxy.tools.deps.mulled.mulled_build_tool module
- galaxy.tools.deps.mulled.mulled_search module
- galaxy.tools.deps.mulled.util module
- Module contents
- galaxy.tools.deps.resolvers package
- Submodules
- galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
- galaxy.tools.deps.resolvers.conda module
- galaxy.tools.deps.resolvers.galaxy_packages module
- galaxy.tools.deps.resolvers.homebrew module
- galaxy.tools.deps.resolvers.lmod module
- galaxy.tools.deps.resolvers.modules module
- galaxy.tools.deps.resolvers.resolver_mixins module
- galaxy.tools.deps.resolvers.tool_shed_packages module
- galaxy.tools.deps.resolvers.unlinked_tool_shed_packages module
- Module contents
- Submodules
- galaxy.tools.deps.brew_exts module
- galaxy.tools.deps.brew_util module
- galaxy.tools.deps.commands module
- galaxy.tools.deps.conda_compat module
- galaxy.tools.deps.conda_util module
- galaxy.tools.deps.containers module
- galaxy.tools.deps.dependencies module
- galaxy.tools.deps.docker_util module
- galaxy.tools.deps.dockerfiles module
- galaxy.tools.deps.installable module
- galaxy.tools.deps.requirements module
- galaxy.tools.deps.singularity_util module
- galaxy.tools.deps.views module
- Module contents
- Subpackages
- galaxy.tools.linters package
- Submodules
- galaxy.tools.linters.citations module
- galaxy.tools.linters.command module
- galaxy.tools.linters.cwl module
- galaxy.tools.linters.general module
- galaxy.tools.linters.help module
- galaxy.tools.linters.inputs module
- galaxy.tools.linters.outputs module
- galaxy.tools.linters.stdio module
- galaxy.tools.linters.tests module
- galaxy.tools.linters.xml_order module
- Module contents
- galaxy.tools.locations package
- galaxy.tools.parser package
- Submodules
- galaxy.tools.parser.cwl module
- galaxy.tools.parser.factory module
- galaxy.tools.parser.interface module
- galaxy.tools.parser.output_actions module
- galaxy.tools.parser.output_collection_def module
- galaxy.tools.parser.output_objects module
- galaxy.tools.parser.util module
- galaxy.tools.parser.xml module
- galaxy.tools.parser.yaml module
- Module contents
- galaxy.tools.toolbox package
- galaxy.tools.verify package
Submodules¶
galaxy.tools.fetcher module¶
galaxy.tools.lint module¶
This modules contains the functions that drive the tool linting framework.
-
galaxy.tools.lint.
lint_tool_source
(tool_source, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)[source]¶
galaxy.tools.lint_util module¶
galaxy.tools.loader module¶
-
galaxy.tools.loader.
load_tool
(path)¶
-
galaxy.tools.loader.
load_tool_with_refereces
(path)¶ Load XML documentation from file system and preprocesses XML macros.
Return the XML representation of the expanded tree and paths to referenced files that were imported (macros).
-
galaxy.tools.loader.
raw_tool_xml_tree
(path)¶ Load raw (no macro expansion) tree representation of XML represented at the specified path.
galaxy.tools.loader_directory module¶
Utilities for loading and reasoning about unparsed tools in directories.
-
galaxy.tools.loader_directory.
find_possible_tools_from_path
(path, recursive=False, enable_beta_formats=False)[source]¶ Walk a directory and find potential tool files.
-
galaxy.tools.loader_directory.
is_a_yaml_with_class
(path, classes)[source]¶ Determine if a file is a valid YAML with a supplied
class
entry.
-
galaxy.tools.loader_directory.
is_tool_load_error
(obj)[source]¶ Predicate to determine if object loaded for tool is a tool error.
-
galaxy.tools.loader_directory.
load_tool_elements_from_path
(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]¶ Walk a directory and load tool XML elements.
-
galaxy.tools.loader_directory.
load_tool_sources_from_path
(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]¶ Walk a directory and ToolSource objects.
-
galaxy.tools.loader_directory.
looks_like_a_cwl_artifact
(path, classes=None)[source]¶ Quick check to see if a file looks like it may be a CWL artifact.
-
galaxy.tools.loader_directory.
looks_like_a_tool_cwl
(path)[source]¶ Quick check to see if a file looks like it may be a CWL tool.