immuneML.api.galaxy package¶
Submodules¶
immuneML.api.galaxy.ApplyGenModelTool module¶
- class immuneML.api.galaxy.ApplyGenModelTool.ApplyGenModelTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.DataSimulationTool module¶
- class immuneML.api.galaxy.DataSimulationTool.DataSimulationTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.DatasetGenerationOverviewTool module¶
- class immuneML.api.galaxy.DatasetGenerationOverviewTool.DatasetGenerationOverviewTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
DatasetGenerationOverviewTool is an alternative to running ImmuneMLApp directly. This tool is meant to be used as an endpoint for Galaxy tool that will create a Galaxy collection out of a dataset in immuneML format.
This tool accepts a path to a YAML specification which uses a single dataset, and runs the ExploratoryAnalysisInstruction with optional reports. The created dataset will be located in the supplied output directory, under the ‘galaxy_dataset’ folder. The main dataset file will have the name of the dataset given in the specification and has an extension .yaml.
immuneML.api.galaxy.DatasetGenerationTool module¶
- class immuneML.api.galaxy.DatasetGenerationTool.DatasetGenerationTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
DatasetGenerationTool is an alternative to running ImmuneMLApp directly. It accepts a path to YAML specification and a path to the output directory and generates the dataset according to the given specification. The created dataset will be located under supplied output directory, under galaxy_dataset folder. The main dataset file will have the name of the dataset given in the specification and has an extension .yaml.
This tool is meant to be used as an endpoint for Galaxy tool that will create a Galaxy collection out of a dataset in immuneML format.
Specification for this tool is the same as for the DatasetExportInstruction, except it can create only one dataset with one format at the time.
immuneML.api.galaxy.GalaxyMLApplicationTool module¶
- class immuneML.api.galaxy.GalaxyMLApplicationTool.GalaxyMLApplicationTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.GalaxySimulationTool module¶
- class immuneML.api.galaxy.GalaxySimulationTool.GalaxySimulationTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
GalaxySimulationTool is an alternative to running immuneML with the simulation instruction directly. It accepts a YAML specification file and a path to the output directory. It implants the signals in the dataset that was provided either as an existing dataset with a set of files or in the random dataset as described in the specification file.
This tool is meant to be used as an endpoint for Galaxy tool that will create a Galaxy collection out of a dataset in immuneML format that can be readily used by other immuneML-based Galaxy tools.
The specification supplied for this tool is identical to immuneML specification, except that it can include only one instruction which has to be of type ‘Simulation’:
immuneML.api.galaxy.GalaxyTool module¶
immuneML.api.galaxy.GalaxyTrainGenModel module¶
- class immuneML.api.galaxy.GalaxyTrainGenModel.GalaxyTrainGenModel(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.GalaxyTrainMLModel module¶
- class immuneML.api.galaxy.GalaxyTrainMLModel.GalaxyTrainMLModel(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.GalaxyYamlTool module¶
- class immuneML.api.galaxy.GalaxyYamlTool.GalaxyYamlTool(specification_path: Path, result_path: Path, **kwargs)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.RepertoireClassificationTool module¶
- class immuneML.api.galaxy.RepertoireClassificationTool.RepertoireClassificationTool(args, result_path: Path)[source]¶
Bases:
GalaxyTool
immuneML.api.galaxy.Util module¶
immuneML.api.galaxy.build_apply_gen_model_specs module¶
immuneML.api.galaxy.build_clustering_yaml module¶
immuneML.api.galaxy.build_dataset_overview_yaml module¶
immuneML.api.galaxy.build_dummy_data_simulation_yaml module¶
immuneML.api.galaxy.build_ligo_yaml module¶
immuneML.api.galaxy.build_ml_application_yaml module¶
immuneML.api.galaxy.build_train_gen_model_specs module¶
immuneML.api.galaxy.build_train_ml_model_yaml module¶
- immuneML.api.galaxy.build_train_ml_model_yaml.get_ml_method_spec(ml_method_class, model_selection_n_folds=5)[source]¶