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Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
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Based on SOC occupation classification
Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
Assemble Galaxy workflow test fixtures and assertions.
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
Path from a CWL Workflow to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the CWL → GALAXY pipeline in order, in a per-run working directory.
| name | freeform-summary-to-galaxy-test-plan |
| description | Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
freeform-summary. Produced by interview-to-freeform-summary, summarize-paper. Free-form source summary from summarize-paper or interview-to-freeform-summary; carries methods, sample data, parameters, and expected outputs that seed test intent.freeform-galaxy-interface. Produced by freeform-summary-to-galaxy-interface. Galaxy interface brief from freeform-summary-to-galaxy-interface that pins workflow inputs, outputs, and labels the plan binds assertions to.freeform-galaxy-data-flow. Produced by freeform-summary-to-galaxy-data-flow. Galaxy data-flow brief from freeform-summary-to-galaxy-data-flow that pins abstract operations and collection choices the plan must respect.iwc-comparison-notes. Produced by compare-against-iwc-exemplar. Structural diff guidance from compare-against-iwc-exemplar; steers the plan toward IWC-aligned testable checkpoints and fixture shapes.iwc-exemplar-gxformat2. Produced by compare-against-iwc-exemplar. Cleaned gxformat2 view of the nearest IWC exemplar from compare-against-iwc-exemplar; pattern-match its labels, collection identifiers, and tested checkpoints. Absent when no nearest exemplar was found.galaxy-test-plan as galaxy-test-plan.yml. Format: yaml. Schema: galaxy-workflow-test-plan. Reviewable Galaxy workflow test plan (see galaxy-workflow-test-plan): synthesized test cases with job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.references/schemas/galaxy-workflow-test-plan.schema.json: Schema file copied verbatim into the bundle. Output contract: the emitted plan conforms to galaxy-workflow-test-plan. Cast bundles the JSON Schema so the skill carries its output shape; validate with foundry validate-galaxy-workflow-test-plan.references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Choose which workflow outputs and promoted checkpoints make meaningful assertions when no upstream test evidence exists. Use when: deciding which outputs to assert, which checkpoints to promote, and which labels the plan should assume.references/notes/iwc-shortcuts-anti-patterns.md: Research note copied verbatim into the bundle. Distinguish accepted IWC-style test shortcuts from assertion smells while synthesizing assertions from intent. Use when: considering existence-only, size-only, image-dimension, or tolerant output checks, or recording an omission.references/notes/iwc-test-data-conventions.md: Research note copied verbatim into the bundle. Describe job-input fixtures, remote-URL-first locations, hashes, and collection input shapes the plan should record as fixture provenance. Use when: recording job inputs or fixture provenance, or deciding whether a fixture belongs in test-data, Zenodo, ENA/SRA, or CVMFS.references/notes/planemo-asserts-idioms.md: Research note copied verbatim into the bundle. Pick the assertion family and tolerance that fit each synthesized expected output by output type. Use when: turning an expected output into assertion intent and a tolerance.references/notes/planemo-workflow-test-architecture.md: Research note copied verbatim into the bundle. Keep the plan addressable by stable labels and artifacts Planemo can connect back to invocations, jobs, and outputs. Use when: recording the labels and checkpoints the downstream test must address.references/schemas/tests-format.schema.json: Schema file copied verbatim into the bundle. Use the Galaxy workflow tests schema as the assertion-family vocabulary referenced by the plan's assertion intent. Use when: naming an assertion family or compare operator for a synthesized expected output.galaxy-test-plan.yml before returning it: run foundry validate-galaxy-workflow-test-plan galaxy-test-plan.yml from @galaxy-foundry/foundry. If the command is not on PATH, run npx --package @galaxy-foundry/foundry foundry validate-galaxy-workflow-test-plan galaxy-test-plan.yml. This checks artifact galaxy-test-plan against the galaxy-workflow-test-plan schema.Synthesize a Galaxy workflow test plan from a free-form source summary and the Galaxy interface and data-flow briefs. The output is a reviewable handoff conforming to galaxy-workflow-test-plan, not a concrete tests-format file: it records test cases, job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and intentional omissions so implement-galaxy-workflow-test can author the final Galaxy test artifact.
This is the structural difference from nextflow-test-to-galaxy-test-plan and cwl-test-to-galaxy-test-plan. Those skills translate existing upstream test evidence — nf-test snapshots, CWL job files and expected outputs — into a Galaxy plan. A free-form source has no upstream test fixtures to convert, so this skill synthesizes the plan from workflow intent and scenario-level expected outputs: the methods, sample data, parameters, and "expected results" recorded in the free-form summary, plus the testable structure the interface/data-flow briefs and the nearest IWC exemplar imply.
Set the plan's source.derived_from to intent (not test-evidence) and each synthesized assertion's evidence to intent; most synthesized assertions are confidence: medium or low. Where the summary does carry a concrete expected value (a known count, a named output token, a published figure), record it as expected_value and raise the confidence.
This skill consumes the template-era briefs, not the concrete workflow draft or the resolved test-data refs — those exist in the harness run-state by the time the plan is authored, but they are reconciled downstream rather than here. So:
label_status to assumed (or unresolved when even the brief is silent) and the plan's workflow.label_source to interface-brief. implement-galaxy-workflow-test reconciles these against the real draft labels and the workflow-label cross-check.storage: unresolved and location: null when the free-form summary names test data only by description; capture what is known (a dataset name, an accession, a Zenodo DOI, a rough size) in fixture.provenance so test-data resolution and the implement skill can act on it. Use iwc-test-data-conventions for the storage classes and the remote-URL-first convention.When a binding or fixture cannot be settled from the briefs, add an unresolved[] entry (with blocking: true when the final test cannot be authored without it) rather than inventing a label or a URL.
For each expected output the briefs expose, pick the assertion family by output type per planemo-asserts-idioms and a defensible tolerance. When the only exposed output is weakly assertable (a stochastic plot, an opaque binary), consult galaxy-workflow-testability-design: prefer recording assertion intent against a stronger promoted checkpoint, and when you settle for a weak check, record the weaker outputs in omissions[] with a rationale rather than asserting around them. Check each shortcut against iwc-shortcuts-anti-patterns so an existence-only or size-only intent is a deliberate choice.
Keep the plan addressable by stable labels and artifacts (planemo-workflow-test-architecture) so the downstream test, run, and debug skills can connect assertions back to invocations and outputs.