galaxy.tools package

Subpackages

Submodules

galaxy.tools.fetcher module

class galaxy.tools.fetcher.ToolLocationFetcher[source]

Bases: object

to_tool_path(path_or_uri_like, **kwds)[source]

galaxy.tools.hash module

galaxy.tools.hash.build_tool_hash(as_dict)[source]

galaxy.tools.lint module

This modules contains the functions that drive the tool linting framework.

class galaxy.tools.lint.LintContext(level, skip_types=[], object_name=None)[source]

Bases: object

error(message, *args)[source]
failed(fail_level)[source]
info(message, *args)[source]
lint(name, lint_func, lint_target)[source]
valid(message, *args)[source]
warn(message, *args)[source]
galaxy.tools.lint.lint_tool_source(tool_source, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)[source]
galaxy.tools.lint.lint_tool_source_with(lint_context, tool_source, extra_modules=[])[source]
galaxy.tools.lint.lint_xml(tool_xml, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)[source]
galaxy.tools.lint.lint_xml_with(lint_context, tool_xml, extra_modules=[])[source]

galaxy.tools.lint_util module

galaxy.tools.lint_util.is_datasource(tool_xml)[source]

Returns true if the tool is a datasource tool

galaxy.tools.loader module

galaxy.tools.loader.imported_macro_paths(root)[source]
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.template_macro_params(root)[source]

Look for template macros and populate param_dict (for cheetah) with these.

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.

galaxy.tools.loader_directory.looks_like_a_tool_xml(path)[source]

Quick check to see if a file looks like it may be a Galaxy XML tool file.

galaxy.tools.loader_directory.looks_like_a_tool_yaml(path)[source]

Quick check to see if a file looks like it may be a Galaxy YAML tool file.

Module contents