القائمة
Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
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.
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).
| name | advance-galaxy-draft-step |
| description | Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
galaxy-workflow-draft. Schema: galaxy-workflow-draft. Produced by advance-galaxy-draft-step, apply-galaxy-workflow-changeset, cwl-summary-to-galaxy-template, freeform-summary-to-galaxy-template, implement-galaxy-tool-step, nextflow-summary-to-galaxy-template, repair-galaxy-draft-topology. gxformat2 draft (see galaxy-workflow-draft-format) mutated in-place across iterations; topology is fully concrete, individual tool steps may still carry TODO_* sentinels and _plan_* planning fields.open-requirements-ledger. Produced by advance-galaxy-draft-step, apply-galaxy-workflow-changeset, compare-against-iwc-exemplar, cwl-summary-to-galaxy-data-flow, cwl-summary-to-galaxy-interface, cwl-summary-to-galaxy-template, freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-interface, freeform-summary-to-galaxy-template, implement-galaxy-tool-step, interview-to-galaxy-workflow-changeset, nextflow-summary-to-galaxy-data-flow, nextflow-summary-to-galaxy-interface, nextflow-summary-to-galaxy-reference-data, nextflow-summary-to-galaxy-template, repair-galaxy-draft-topology. Carried obligations ledger open-requirements-ledger: after implementing the chosen step, read it for a new open blocking entry implement-galaxy-tool-step appended (the step's declared output can't be computed from its wired inputs), and count open blocking entries for the escalation convergence gate.galaxy-workflow-draft as galaxy-workflow-draft.gxwf.yml. Format: yaml. Schema: galaxy-workflow-draft. Same draft with one additional step concretized (one loop iteration). Once every step is concrete, draft-next-step reports draft: false and the harness exits the loop.galaxy-workflow as galaxy-workflow.gxwf.yml. Format: yaml. Concrete gxformat2 workflow (class: GalaxyWorkflow) extracted from the fully-concretized draft at loop endstate via draft-extract: drafty steps dropped, _plan_* planning fields stripped, class promoted. The runnable, testable artifact that downstream Molds (implement-galaxy-workflow-test, validate-galaxy-workflow, run-workflow-test) consume.open-requirements-ledger as open-requirements.ledger.yml. Format: yaml. Same ledger carried through the iteration: a blocking entry implement-galaxy-tool-step appended is routed to repair-galaxy-draft-topology and returns marked resolved or surrendered.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/clireferences/cli/draft-next-step.json: CLI command reference packaged as a sidecar. Deterministically pick the next drafty step (or report no remaining work). The orchestrator owns the loop oracle so the harness reduces to while draft: invoke skill. Use when: at the start of every iteration, before any per-step work.references/notes/open-requirements-ledger.md: Research note copied verbatim into the bundle. Recognize the blocking entry implement-galaxy-tool-step appends (its shape and open | resolved | surrendered status) so the orchestrator can detect the raised computability gap, count open blocking entries for the convergence gate, and escalate to repair-galaxy-draft-topology.references/schemas/galaxy-workflow-draft.schema.json: Schema file copied verbatim into the bundle. In/out contract: the draft this Mold reads and mutates one step per iteration conforms to galaxy-workflow-draft. Cast bundles the JSON Schema alongside the draft-validate CLI checks.references/cli/draft-extract.json: CLI command reference packaged as a sidecar. At loop endstate, extract the concrete gxformat2 workflow from the fully-concretized draft — drop drafty steps, strip _plan_* fields, promote class to GalaxyWorkflow — and write it as the runnable galaxy-workflow.gxwf.yml. Use when: draft-next-step reports draft: false (no remaining drafty steps).references/cli/draft-validate.json: CLI command reference packaged as a sidecar. Validate the mutated draft against draft-contract rules and, with --concrete, also gate the extracted concrete subset (including the step just implemented) against full gxformat2. Use when: after implementing or modifying the chosen step in the draft.references/notes/galaxy-tool-job-failure-reference.md: Research note copied verbatim into the bundle. Classify draft-validate diagnostics against wrapper-defined runtime failure semantics so the iteration routes back to the right authoring surface (implementation vs. wrapper choice). Use when: draft-validate fails after a step has been implemented, or when a selected wrapper has explicit failure semantics that may surface at runtime.references/schemas/galaxy-tool-summary.schema.json: Schema file copied verbatim into the bundle. Bind the chosen step against the deterministic tool summary manifest emitted by summarize-galaxy-tool — read parsed_tool for ports/datatypes and input_schemas.workflow_step_linked for valid step tool_state shape. Use when: after a wrapper has been resolved for the chosen step and before implementing it.galaxy-workflow-draft.gxwf.yml for artifact galaxy-workflow-draft against the galaxy-workflow-draft schema when a validator is available.Orchestrator skill for the per-step Galaxy authoring loop. One invocation advances the gxformat2 draft by one step: pick → resolve a wrapper → summarize the wrapper → implement the step → validate. The harness loop reduces to while (gxwf draft-next-step <wf>).draft: invoke skill.
This skill is single-entry, single-exit: it owns the loop oracle (draft-next-step) and the per-step validator (draft-validate --concrete). Iterations terminate when the draft has no remaining drafty steps; on that terminal call the skill extracts the concrete galaxy-workflow.gxwf.yml (via draft-extract) — that promoted-class workflow, not the -draft file, is what downstream skills test and run — and the harness then drops out of the loop and proceeds to terminal validation via validate-galaxy-workflow.
draft: false, the loop is done: run draft-extract to emit the concrete galaxy-workflow.gxwf.yml (drafty steps dropped, _plan_* stripped, class promoted to GalaxyWorkflow), then return. Otherwise carry the chosen step id forward.owner/repo path (Filter1, sort1, Cut1, Show beginning1, collection ops, __APPLY_RULES__):
Built-in / stock — the bare id is the wrapper identity; it does not route through discover-shed-tool (Tool Shed search) or author-galaxy-tool-wrapper. Only its concrete version needs resolving: the shed serves stock tools by bare id, but its TRS version-list endpoint can't auto-resolve the version, so read it from a populated cache via galaxy-tool-cache list or take a known pin from the step plan — never hand-guess a stock version. summarize-galaxy-tool then performs the bare-id add/summarize with that explicit --tool-version.
Tool Shed wrapper — branch on whether the template already pinned wrapper identity (see the tiers in galaxy-workflow-draft-format):
tool_id is concrete and tool_version is TODO. Treat the pin as a strong seed: confirm it via discover-shed-tool and resolve the changeset, correcting the tool_id only if discovery contradicts the pin (a pinned id is high-confidence template evidence, not a guess to re-derive from scratch).tool_id is TODO. Search fresh: run discover-shed-tool against the step's _plan_* context.Either way, if no acceptable shed candidate emerges, fall through to author-galaxy-tool-wrapper.
TODO_* / _plan_* slots into a concrete tool_id (confirming or correcting any pinned identity), tool_version, tool_state, and wrapper-determined port names.open blocking entry implement-galaxy-tool-step appended against this step — a declared output that can't be computed from its wired inputs. draft-validate cannot catch this: the connection graph knows ports connect, not what they carry, so the draft validates green even though the step can't run. If such an entry is present, escalate to repair-galaxy-draft-topology for a bounded repair (insert a producer/sub-path or honestly narrow the output); it marks the entry resolved, or surrendered when no producer is reachable. Each escalation must strictly reduce the open blocking-entry count, under a hard escalation cap; track both in the ledger's topology_repair block (increment escalations, append the post-repair open count to open_history, surrender once escalations reaches cap). A surrendered entry stays open and is written into the final draft as a labelled gap rather than fabricated. Then return — the next iteration resumes the loop, realizing any draft-tier steps the repair inserted. With no new blocking entry, continue to validation.--concrete over the mutated draft. On green, return; the next iteration starts at step 1. On red, route per the failure-routing rules below.draft-validate --concrete failures fall into three buckets:
tool_state) — re-enter implement-galaxy-tool-step with the diagnostic._plan_* contract — wrong datatype, missing parameter, incompatible collection shape) — back out to step 2 and pick a different wrapper, either via discover-shed-tool with refined criteria or by escalating to author-galaxy-tool-wrapper.These are red-draft-validate buckets. The fourth escalation path — a step output uncomputable from its wired inputs — is not one of them: the draft validates green there, so it is detected from the ledger in step 5 above, not from a validation failure.
Consult galaxy-tool-job-failure-reference when the wrapper has explicit failure semantics that affect routing — strict-shell behavior, dynamic outputs, or non-default stdio rules can present as wrapper-choice mismatches even when the static shape validates.
Prior pipelines expressed the iteration as four entries: a discover-or-author branch plus summarize-galaxy-tool, implement-galaxy-tool-step, and validate-galaxy-step. Collapsing them into one orchestrator keeps the per-iteration narrative — including the discover-or-author branch and the failure-routing rules — in a single procedural surface that the skill can render coherently. Leaf skills stay independently castable for ad-hoc invocation; only the pipeline shape changes.