Parameters

The Parameters class is used to define the input parameters for a Galaxy tool.

notebook = Dataset(path="tests/test_files/test_jupyter_notebook.ipynb")
test_tool = Tool(TEST_INT_TOOL_ID)
params = Parameters()
params.add_input("mode|mode_select", "previous")
params.add_input("ipynb", notebook)
params.add_input("run_it", True)
link = test_tool.run_interactive(data_store=store, params=params, check_url=False)

You can remove an existing input value with remove_input() or change the value with change_input_value().

Workflow Parameters

The WorkflowParameters class is specifically designed for passing inputs and parameters to Galaxy workflows. It provides a more explicit, bioblend-style approach to define workflow-level inputs and parameters for individual steps within a workflow.

Workflow-level Inputs (`add_workflow_input`)

Use add_workflow_input to provide values for the overall workflow inputs, which are typically identified by numerical IDs (e.g., “0”, “1”) as defined in the workflow. These can be datasets, dataset collections, or simple values.

from nova.galaxy.parameters import WorkflowParameters
from nova.galaxy.dataset import Dataset, DatasetCollection

workflow_params = WorkflowParameters()

# Adding a dataset as a workflow input (input ID "0")
my_dataset = Dataset(id="your_dataset_id")
workflow_params.add_workflow_input("0", my_dataset)

# Adding a dataset collection as a workflow input (input ID "1")
my_collection = DatasetCollection(id="your_collection_id")
workflow_params.add_workflow_input("1", my_collection)

# Adding a simple text value as a workflow input (input ID "2")
workflow_params.add_workflow_input("2", "my_text_input")

Step-level Parameters (`add_step_param`)

Use add_step_param to set parameters for specific steps within the workflow. These are identified by the step’s ID (e.g., “2”, “4”) and a parameter path (e.g., “input”, “series_0|input_mode|export_folder”).

from nova.galaxy.parameters import WorkflowParameters
from nova.galaxy.dataset import Dataset

workflow_params = WorkflowParameters()

# Setting a parameter for step "2" with parameter path "input"
# This could be a dataset, dataset collection, or simple value
input_for_step_2 = Dataset(id="another_dataset_id")
workflow_params.add_step_param("2", "input", input_for_step_2)

# Setting a text parameter for step "3" with parameter path "some_option"
workflow_params.add_step_param("3", "some_option", "value_for_option")

# Setting a list of datasets for a parameter in step "4"
list_of_datasets = [Dataset(id="ds1"), Dataset(id="ds2")]
workflow_params.add_step_param("4", "multiple_inputs", list_of_datasets)

When running a workflow, you pass an instance of WorkflowParameters to the Workflow.run() method.