القائمة
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
| 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.
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.