gxformat2 workflow inputs
Top-level inputs: names the values a caller supplies to a Galaxy workflow. Choose the input type from the value the workflow consumes, and give it a stable name that a test can use as a job: key. See galaxy-workflow-testability-design for the test interface.
Match the input’s shape
| Value | gxformat2 type | Other fields to consider |
|---|---|---|
| One dataset | data | format for accepted Galaxy datatypes |
| A dataset collection | collection | collection_type for its shape, format for member datatypes |
| A scalar parameter | string, int, float, or boolean | default or choices where appropriate |
Use data for a single dataset input. It is the common spelling in Galaxy’s gxformat2 workflow fixtures and in normalized gxformat2 exports. gxformat2-schema lists other accepted input types.
For a collection, declare the shape the workflow needs. Galaxy defaults an omitted collection_type to list; list:paired means a list of paired datasets. The IWC CellPlex workflow has two list:paired FASTQ inputs and a separate list of CSV sample mappings. See galaxy-collection-semantics for other shapes and galaxy-datatypes-conf for datatype extensions.
Set defaults and constraints deliberately
optional: true permits a missing input. default supplies a value when an input is missing or null; it does not itself make the input optional. The IWC Scanpy workflow combines format: [mtx] for its Matrix dataset with an optional text parameter whose default is MT-.
For text parameters, restrictions defines a closed choice list, suggestions offers choices while allowing other text, and restrictOnConnections derives choices from connected select inputs.
For int and float parameters, set min and max to inclusive bounds. Either bound can be omitted. Foundry targets gxwf 1.13.1 or newer, which converts these bounds to Galaxy in_range validators and recovers them on export. See gxwf for installation.
The older vendored JSON Schema in gxformat2-schema omits fields such as restrictions, suggestions, and restrictOnConnections. Its field list does not cover every supported input constraint.
After import or conversion, inspect the effective input names, types, collection shapes, defaults, and constraints. Run a workflow test with representative job: values to check the interface Galaxy actually uses. iwc-test-data-conventions covers fixture shapes.