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Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.
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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.
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 | summarize-galaxy-tool |
| description | Pull JSON schema, container, source, inputs/outputs for a Galaxy tool. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
galaxy-tool-pin. Schema: galaxy-tool-discovery. Produced by discover-shed-tool. Pin identifying which cached ParsedTool to summarize: a Tool Shed pin from discover-shed-tool (owner/repo/tool + version), or a bare/stock id for a built-in Galaxy tool (e.g. Filter1, Cut1, collection ops) that resolves against the shed by the bare id. Authored UDTs from author-galaxy-tool-wrapper bypass this Mold.galaxy-tool-summary as galaxy-tool-summary.json. Format: json. Schema: galaxy-tool-summary. Deterministic Galaxy tool summary manifest emitted by galaxy-tool-cache summarize: cache provenance, embedded ParsedTool, generated input JSON Schemas.galaxy-tool-cache (galaxy-tool-cache). npm install -g @galaxy-tool-util/cli@^1.8.1.
Ephemeral run: npx --yes --package @galaxy-tool-util/cli@1.8.1 galaxy-tool-cache.
Check: galaxy-tool-cache --help | grep -q summarize.
Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli
Bundled reference: references/cli/galaxy-tool-cache.md.references/cli/summarize.json: CLI command reference packaged as a sidecar. Emit the deterministic galaxy-tool-summary manifest for the cached pin; this Mold runs the command rather than hand-authoring the manifest. Use when: once the pin is confirmed present in the cache.references/cli/galaxy-tool-cache.md: CLI tool reference copied verbatim into the bundle. Runtime that emits the tool summary; the Mold's entire job is invoking it against a populated cache. Install before driving the skill.references/notes/galaxy-tool-summary-input-source.md: Research note copied verbatim into the bundle. Treat cached ParsedTool JSON from galaxy-tool-cache as the v1 input source for Galaxy tool summaries.references/schemas/galaxy-tool-summary.schema.json: Schema file copied verbatim into the bundle. Validate the manifest emitted by galaxy-tool-cache summarize before handing it to downstream step Molds.references/cli/add.json: CLI command reference packaged as a sidecar. Cache-population precondition: summarize reads an already-cached pin and fails if missing, so add fetches the pin into the cache first. Stock/built-in bare ids resolve against the shed but need an explicit --tool-version. Use when: the requested pin is not yet present in the configured cache directory.references/cli/list.json: CLI command reference packaged as a sidecar. Discover the concrete cached version of a stock/built-in bare id before add/summarize, since the shed's TRS version-list endpoint can't auto-resolve it; never hand-guess a stock version. Use when: the pin is a bare/stock id (no owner/repo) and its concrete version isn't already known.references/notes/component-tool-shed-search.md: Research note copied verbatim into the bundle. Resolve Galaxy tool identity, Tool Shed versioning, and changeset context before summarizing a wrapper. Use when: a tool summary starts from a Tool Shed hit rather than an installed Galaxy tool object.references/schemas/parsed-tool.schema.json: Schema file copied verbatim into the bundle. Resolve field-level questions about the upstream ParsedTool payload embedded under parsed_tool. Use when: a downstream Mold needs a specific input/output/help/citation field from the embedded ParsedTool.galaxy-tool-summary.json before returning it: run foundry validate-galaxy-tool-summary galaxy-tool-summary.json from @galaxy-foundry/foundry. If the command is not on PATH, run npx --package @galaxy-foundry/foundry foundry validate-galaxy-tool-summary galaxy-tool-summary.json. This checks artifact galaxy-tool-summary against the galaxy-tool-summary schema.Read a cached Galaxy ParsedTool object for an existing wrapper and emit a compact tool summary that downstream step implementation can bind to. This skill runs after discover-shed-tool has selected a Tool Shed pin and after the caller has populated galaxy-tool-cache for that pin.
This skill owns the wrapper summarization step only. It does not search the Tool Shed, choose a version, author XML, or decide how a workflow step should use the wrapper. Its job is to preserve the wrapper's executable contract: identity, command shape, inputs, outputs, requirements, tests, and any conditional or data-table behavior that could affect binding.
The v1 input-source decision is galaxy-tool-summary-input-source: read cached ParsedTool JSON, using raw XML only as supporting evidence when the cache object is lossy or ambiguous.
The skill expects:
tool_shed_url, owner, repo, tool_id, version, and changeset_revision; or a bare/stock id for a built-in tool (Filter1, Cut1, Show beginning1, collection ops, __APPLY_RULES__) plus a concrete version.galaxy-tool-cache directory containing the cached ParsedTool JSON for that pin.A single JSON document conforming to galaxy-tool-summary — the deterministic manifest emitted by galaxy-tool-cache summarize from @galaxy-tool-util/cli. Top-level fields: schema_version, tool_id, tool_version, cache_key, source, artifacts, parsed_tool, input_schemas, warnings. The parsed_tool subtree is the upstream parsed-tool payload verbatim; input_schemas.workflow_step and input_schemas.workflow_step_linked carry generated JSON Schemas describing the tool's inputs at workflow-step authoring time.
This skill does not hand-author the manifest — it invokes galaxy-tool-cache summarize against a cache populated for the Tool Shed pin. Wrapper-derived facts that are not yet exposed by upstream ParsedTool (currently: requirements, containers, stdio) flow into the manifest additively as Galaxy upstream extends ParsedTool; no Foundry-side schema change is needed when they ship.
Locate the ParsedTool JSON in the configured galaxy-tool-cache directory using the Tool Shed pin. galaxy-tool-cache summarize reads an already-cached pin — it does not re-fetch — so the pin must be cached first via add (single pin) or populate-workflow (the loop driver's whole-draft form). If the cache entry is missing, run add for the pin rather than silently re-searching the Tool Shed; fail early if add cannot resolve it.
Confirm the cached identity matches the requested pin. If the cache exposes a tool id or version that conflicts with the pin, emit a hard failure rather than summarizing the wrong wrapper.
Built-in / stock tools. When the pin is a bare/stock id (no owner/repo — Filter1, Cut1, Show beginning1, collection ops, __APPLY_RULES__), the same cache flow applies with the bare id: add fetches it from the Tool Shed by the bare id and summarize reads it back. The shed's TRS version-list endpoint can't auto-resolve a stock version, so pass an explicit --tool-version to both. Discover that concrete version from a populated cache via list (or a known pin carried in the step plan) — never hand-guess a stock version. If no concrete version can be resolved from the cache or a known pin, surface it as an unmet requirement rather than inventing one.
Populate source from the discovery pin and cache metadata. Populate tool from the parsed wrapper identity fields, not from the search hit. Search hits can omit version and changeset detail.
Keep both forms when they differ:
id for human matching.Read <requirements> into structured package/container requirements. Preserve requirement type, name, version, and any container URI or resolver hints exposed by the cache.
Do not invent Bioconda equivalences here. Equivalence inference belongs to author-galaxy-tool-wrapper when authoring a new UDT. Existing wrapper summaries report what the wrapper declares.
Preserve the command template enough for downstream binding to understand which inputs and parameters are consumed. Record strict-shell, stdio regexes, exit-code handling, environment variables, and dynamic output behavior when present.
The command summary should be readable, but lossy prose is not enough. Keep template fragments and wrapper flags where they affect required inputs, output discovery, or runtime failure classification.
For every wrapper input parameter, emit:
name and label/help text when available.data, data_collection, select, integer, float, boolean, text, conditional section, repeat, section).Nested conditionals must preserve branch ownership. Do not flatten when branches into independent parameters without recording the controlling selector and branch value.
For every output and collection output, emit:
from_work_dir or discovery rule when available.If output discovery depends on runtime filenames, record that as a warning for downstream test and debug skills.
Summarize wrapper tests into input fixture expectations, parameter settings, and output assertions. Do not treat wrapper tests as workflow tests; they are evidence about legal parameter combinations and output behavior.
Preserve citations, help text, and upstream URLs when present because they help resolve ambiguous wrappers during review.
Warnings should identify missing or lossy surfaces, especially: