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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: InstallationTarget)[source]
Bases:
BaseShedToolDataTableManager- app: InstallationTarget
- 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.
- get_target_install_dir(tool_shed_repository: ToolShedRepository)[source]
- install_tool_data_tables(tool_shed_repository: ToolShedRepository, tool_index_sample_files)[source]
galaxy.tool_shed.tools.tool_validator module
- class galaxy.tool_shed.tools.tool_validator.ToolValidator(app: BasicSharedApp | InstallationTarget)[source]
Bases:
object- __init__(app: BasicSharedApp | InstallationTarget)[source]