القائمة
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
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
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.
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
Assemble Galaxy workflow test fixtures and assertions.
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 | run-workflow-test |
| description | Execute a workflow's tests via Planemo; emit structured pass/fail and outputs. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
workflow-test-result as workflow-test-result.json. Format: json. Structured pass/fail plus captured evidence — Planemo result, invocation/history/workflow ids, artifact paths, Galaxy mode, and (on failure) the observed modality and next reference surface — for debug-galaxy-workflow-output.gxwf (gxwf). npm install -g '@galaxy-tool-util/cli@^1.8.1'.
Ephemeral run: npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf.
Check: gxwf --help | grep -q draft-validate.
Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cliplanemo (planemo). uv tool install planemo==0.75.45 (or pip install planemo==0.75.45).
Ephemeral run: uvx --from planemo==0.75.45 planemo.
Check: planemo --version.
Docs: https://planemo.readthedocs.io/
Bundled reference: references/cli/planemo.md.references/cli/planemo.md: CLI tool reference copied verbatim into the bundle. Runtime that executes the Galaxy or CWL workflow test; install before driving the harness.references/schemas/tests-format.schema.json: Schema file copied verbatim into the bundle. Validate Galaxy workflow test files before starting a Planemo or Galaxy-backed execution.references/cli/validate-tests.json: CLI command reference packaged as a sidecar. Run static schema and workflow-label checks before expensive workflow execution. Use when: before invoking Planemo when a Galaxy workflow test file is present.references/notes/galaxy-workflow-invocation-failure-reference.md: Research note copied verbatim into the bundle. Preserve invocation identifiers and state summaries needed to inspect workflow-level runtime failures after Planemo returns. Use when: planemo reports a failed, cancelled, missing-output, or ambiguous workflow invocation result.references/notes/planemo-asserts-idioms.md: Research note copied verbatim into the bundle. Interpret assertion failures and choose the right fast inner-loop command before full reruns. Use when: a workflow test file exists and the task is to run, iterate, or classify its test assertions.references/notes/planemo-workflow-test-architecture.md: Research note copied verbatim into the bundle. Run workflow tests while preserving Planemo structured artifacts, Galaxy mode, invocation id, history id, and API follow-up context. Use when: choosing between managed Galaxy, external Galaxy, full test runs, existing invocation checks, or direct workflow runs.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.
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.--galaxy_branch off the command unless the user or the harness supplied a specific branch, and never guess a release_* value — Planemo's default targets the newest Galaxy, which is the only version guaranteed to understand every construct a freshly authored workflow can contain. If a branch was supplied, record it in the output so a later failure can be read against it.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 skill consumes.Keep this skill'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.