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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)[source]¶
Bases:
object
- __init__(app: StructuredApp)[source]¶
- generate_repository_info_elem(tool_shed: str, repository_name: str, changeset_revision: str, owner: str, parent_elem=None, **kwd) Element [source]¶
Create and return an ElementTree repository info Element.
- generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None, **kwd)[source]¶
- get_tool_index_sample_files(sample_files: List[str]) List[str] [source]¶
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)[source]¶
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)[source]¶
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.
galaxy.tool_shed.tools.tool_validator module¶
- class galaxy.tool_shed.tools.tool_validator.ToolValidator(app)[source]¶
Bases:
object