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galaxy.tool_shed.tools package

Submodules

galaxy.tool_shed.tools.data_table_manager module

galaxy.tool_shed.tools.data_table_manager.ToolDataTableManager

alias of ShedToolDataTableManager

class galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager(app: StructuredApp)

Bases: object

__init__(app: StructuredApp)

generate_repository_info_elem(tool_shed: str, repository_name: str, changeset_revision: str, owner: str, parent_elem=None, **kwd) → Element

Create and return an ElementTree repository info Element.

generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None, **kwd)

get_tool_index_sample_files(sample_files: List[str]) → List[str]

Try to return the list of all appropriate tool data sample files included in the repository.

handle_missing_data_table_entry(relative_install_dir, tool_path, repository_tools_tups)

Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the tool_data_table_conf.xml file. This method is called only from Galaxy (not the tool shed) when a repository is being installed or reinstalled.

handle_sample_tool_data_table_conf_file(filename, persist=False)

Parse the incoming filename and add new entries to the in-memory self.app.tool_data_tables dictionary. If persist is True (should only occur if call is from the Galaxy side, not the tool shed), the new entries will be appended to Galaxy’s shed_tool_data_table_conf.xml file on disk.

get_target_install_dir(tool_shed_repository)

install_tool_data_tables(tool_shed_repository, tool_index_sample_files)

reset_tool_data_tables()

galaxy.tool_shed.tools.tool_validator module

class galaxy.tool_shed.tools.tool_validator.ToolValidator(app)

Bases: object

__init__(app)

check_tool_input_params(repo_dir, tool_config_name, tool, sample_files)

Check all of the tool’s input parameters, looking for any that are dynamically generated using external data files to make sure the files exist.

load_tool_from_config(repository_id, full_path)