The Tools constructor.
- Parameters
-
- Returns
- An instance of a Tool shed repositories object.
| GalaxyToolShedRepositories::checkForUpdates |
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$params | ) |
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Check for updates to the specified repository, or all installed repositories. GET /api/tool_shed_repositories/check_for_updates
- Parameters
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| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- id: the galaxy-side encoded repository ID
- Returns
| GalaxyToolShedRepositories::exportedWorkflows |
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$params | ) |
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Displays a list of dictionaries containing information about this tool shed repository's exported workflows
Corresponds to the Galaxy API/path at GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/ exported_workflows
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- tool_shed_repo_id: Encoded Tool Shed Repository object encoded ID. To obtain a tool shed repository id, please use this class's index() function.
- Returns
- An array containing information about a tool shed repository's exported workflow.
| GalaxyToolShedRepositories::getLatestInstallable |
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$params | ) |
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Get the latest installable revision of a specified repository from a specified Tool Shed.
Corresponds to the Galaxy API/path at POST /api/tool_shed_repositories/get_latest_installable_revision
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- Returns
- A changeset_revision hash (describes the revison 'number' of the tool) i.e 1:7002b364c3f8
1 being the true rev. number (the larger the more changes it's been through, behind the colon is a supposed unique hash string, though collisions happen)
| GalaxyToolShedRepositories::importWorkflow |
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$params | ) |
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Import the specified exported workflow contained in a tool shed repo.
Corresponds to the Galaxy API/method at POST /api/tool_shed_repositories/import_workflow
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available:
- tool_shed_repo_id: The encoded id of the Tool Shed Repository object.
- index: The location of the workflow to import from within the specified toolshed, defaults to 0 the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository.
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- Returns
- An array containing informaiton of the imported workflow.
| GalaxyToolShedRepositories::importWorkflows |
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$params | ) |
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Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy. POST /api/tool_shed_repositories/import_workflows
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- id: the encoded id of the ToolShedRepository object.
- Returns
| GalaxyToolShedRepositories::index |
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Display metadata on external tool shed repositories in galaxy instance
Corresponds to the Galaxy API/path at GET /api/tool_shed_repositories
- Returns
- An array containing metadata on remote toolsheds galaxy instance.
| GalaxyToolShedRepositories::install |
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$params | ) |
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Initiate the installation of a repository. POST /api/tool_shed_repositories/install
- Parameters
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| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- tool_shed_url: The URL for the toolshed whence this repository is being installed.
- name: The name of the tool shed.
- owner: The owner of the tool shed.
- install_tool_dependencies (Optional): True to install tool dependencies.
- tool_panel_section_id (Optional): The unique identifier for an existing tool panel section
- install_repository_dependencies (Optional): True to install repository dependencies.
- new_tool_panel_section_label (Optional): Create a new tool panel section with this label.
- shed_tool_conf (Optional): The shed tool config file to use for this installation.
- changeset (Optional): The changeset to update to after cloning the repository.
- Returns
- A URL linking to the tool shed's installation progress on the local server.
| GalaxyToolShedRepositories::install_repository_revision |
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$params | ) |
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Install a specified repository revision from a specified tool shed repo.
Corresponds to the Galaxy API/path POST /api/tool_shed_repositories/install_repository_revision
- Parameters
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| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- tool_shed_url: The base URL of the Tool Shed from which to install the repository.
- name: The name of the repository.
- owner: The name of the owner of the repository.
- changeset_revision: The changeset_revision of the Repository Meta Data object associated with the Repository.
- new_tool_panel_section_label (Optional): Label of a new section to be added to the Galaxy tool panel in which to load tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id paramter must be an empty string or both must be an empty string. BOTH CANNOT BE USED SIMULTANEOUSLY
- tool_panel_section_id (Optional): Id of the Galaxy tool panel section in which to load tools contained in the Repository. Either this parameter must be an empty string or new_tool_panel_section_label paramter must be an empty string or both must be an empty string. BOTH CANNOT BE USED SIMULTANEOUSLY
- install_repository_dependencies (Optional): Set to True if you want to install repository dependencies defined for the specified repository being installed. The default setting is False.
- install_tool_dependencies (Optional): Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False.
- shed_tool_conf (Optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file (ex: galaxy.ini). At least oneshed-reelated tool panel config file is required to be configured. Setting this paramter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the toolbox from the specified file is used as the installation location (ex: toolbox tool_path="../shed_tools"). If this parameter is not set, a shed-related tool ppanel configuration file will be selected automatically.
| GalaxyToolShedRepositories::repair_repository_revision |
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$params | ) |
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Repair a specified repository revision previously installed into Galaxy
Corresponds to the Galaxy method/path POST /api/tool_shed_repositories/repair_repository_revision
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- tool_shed_url: The base URL of the Tool Shed from which the Repo was installed.
- name: The name of the Repository.
- owner: The owner of the Repository.
- changeset_revision: The changeset_revision of the Repository Meta data object associated with the Repository.
| GalaxyToolShedRepositories::reset_metadata_on_installed_repositories |
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Resets all metadata on all repositories installed.
Corresponds to the Galaxy API/path PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories
| GalaxyToolShedRepositories::show |
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$params | ) |
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Display a dictionary containing information about a specified tool_shed_repository. GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}
- Parameters
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| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- id: the encoded id of the ToolShedRepository object.
- Returns
| GalaxyToolShedRepositories::status |
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$params | ) |
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Display a dictionary containing information about a specified repository's installation status and a list of its dependencies and the status of each. GET /api/tool_shed_repositories/{id}/status
- Parameters
-
| $params | An associative array containing the input parameters for this function. The following parameters are available: |
- id: the repository's encoded id
- Returns
The documentation for this class was generated from the following file:
1.8.6 
