run-workflow-test

Execute an assembled workflow’s test file via planemo and emit a structured pass/fail with the artifacts a debug pass needs. One invocation runs the test once, captures the evidence, and — on failure — classifies the failure modality and names the next reference surface to inspect. It does not repair anything; that is debug-galaxy-workflow-output‘s job.

Sequence

1. Validate before running. When a test file is present, run validate-tests for the static schema and workflow-label checks first. A run is expensive; do not spend one on a test file that fails static validation.
2. Pick the Galaxy mode. Run against a Planemo-managed Galaxy or an existing/external Galaxy. Planemo-managed is the default and needs no pre-provisioned server: planemo test bootstraps its own Galaxy and installs the workflow’s tools from the Tool Shed/conda — so the absence of a running Galaxy is not a reason to skip the run. Use an existing/external Galaxy only when you deliberately want to target one (shared instance, pre-installed heavy tools/reference data, specific credentials). The real cost of the managed path is install/runtime weight (large tools or multi-GB reference databases), which is a deliberate deferral, not an impossibility. Record which mode was used, how tools, workflows, and test data were staged, and the URLs or API credentials a follow-up inspection would need. The choice and its consequences are guided by planemo-workflow-test-architecture.
3. Run and capture. Drive planemo test with structured output enabled. Preserve the invocation id, history id, workflow id, the Planemo structured result, and any test-output artifact paths — these are the inputs the debug Mold consumes.
4. Classify on failure. When the run exits non-zero or reports failed assertions, failed jobs, a failed invocation, missing outputs, or upload/staging problems, identify the observed failure modality and the single next reference surface to open: Planemo result, Galaxy job API, Galaxy invocation API, history contents, or the test assertion report. Use planemo-asserts-idioms to read assertion failures and galaxy-workflow-invocation-failure-reference to preserve invocation identifiers and state.
5. Hand off. Emit the structured summary — green, or red with modality + captured artifacts + the named next surface — for debug-galaxy-workflow-output.

Keep this Mold’s output a faithful record of what happened, not a diagnosis. Mislabeling a staging failure as an assertion failure here sends the debug pass to the wrong reference surface.