Stock-tool CLI support: correct framing, built-in loop branch, node-meta dedup#324
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…li ^1.8.1 The CLI reference pages (the source we cast + expose to skills) framed stock/built-in tools as needing a Galaxy-instance fallback. Stock tools resolve against the Tool Shed by the bare id (galaxy-tool-util-ts #136, released 1.8.1): - add.md: bare/stock ids resolve against the shed; --galaxy-url reframed "fallback" -> alternate source tried after the shed; note --tool-version required for stock ids (shed TRS version-list endpoint 500s, no auto-version); stock example. - summarize.md: bare stock-id support + stock example. - list.md: new page — cache version-confirmation surface. - index.md: pin package_version ^1.8.1 + invoke_fallback @1.8.1; drop the "or a Galaxy instance" source framing. - Re-cast summarize-galaxy-tool: refreshed cli sidecars, SKILL.md install line, _required_tools.json now carries the 1.8.1 pin. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Stock/built-in tools (bare ids: Filter1, Cut1, collection ops, __APPLY_RULES__) resolve against the Tool Shed by bare id, but the shed's TRS version-list endpoint can't auto-resolve their version — so the loop must discover a concrete version and never hand-guess one (the hallucinated-version failure in #323). - summarize-galaxy-tool: accept a bare/stock id as the pin; wire [[list]] as the version-discovery surface; document the bare-id add/summarize flow with explicit --tool-version. list.md now casts into the skill (no longer an orphan). - advance-galaxy-draft-step (step 2): split wrapper resolution — built-in/stock ids skip discover-shed-tool/author and only resolve a version via the cache flow; Tool Shed wrappers keep the identity-pinned/deferred branches. - implement-galaxy-tool-step (steps 2, 4): take stock tool_version from the summary's cached pin, never invent it; built-in collection ops inserted to close shape gaps get a cache-resolved version too. - Re-cast all three Molds (deterministic; no pending LLM step). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Single-source the CLI version in package.json (root + site), the same way schema notes depend on a node package rather than a vendored copy. Bumping 1.7.2 -> 1.8.1 pulls the corrected stock-tool command/option descriptions into @galaxy-tool-util/cli/meta automatically — the site's cli-registry already renders args/options from that meta, so no hand-copying. - package.json + site/package.json: @galaxy-tool-util/cli ^1.7.2 -> ^1.8.1 (schema stays ^1.7.2 to avoid unrelated cast churn). - content/cli/gxwf/index.md: pin package_version ^1.8.1 + invoke_fallback @1.8.1 for parity with galaxy-tool-cache. - Re-cast advance/implement and re-assemble pipeline harnesses to carry the pin. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…li/meta cli-command sidecars now carry description/synopsis/args/options resolved from the package's `meta` subpath (the same browser-safe spec the commander program and --help are built from) — the single source the site's cli-registry already renders from. buildCliSidecar imports `<package>/meta`, matches the program by tool name and the command by name, and embeds them; it falls back to body-only when a package ships no meta subpath (e.g. planemo). With flags now sourced from the package, the galaxy-tool-cache notes drop their hand-authored ## Flags lists (mechanical mirrors of the meta). gxwf/draft-validate keeps its section — it documents --concrete extract+promote semantics and pass-through gating the one-line meta descriptions don't carry. The shared --cache-dir invariant moves to add.md Gotchas so it survives the flag-list drop. Adds a cast-mold regression test for the meta-injection path. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
# Conflicts: # casts/claude/skills/advance-galaxy-draft-step/SKILL.md # casts/claude/skills/advance-galaxy-draft-step/_provenance.json # casts/claude/skills/advance-galaxy-draft-step/_required_tools.json # casts/claude/skills/implement-galaxy-tool-step/SKILL.md # casts/claude/skills/implement-galaxy-tool-step/_provenance.json # casts/claude/skills/implement-galaxy-tool-step/_required_tools.json # casts/claude/skills/pipeline-cwl-to-galaxy/SKILL.md # casts/claude/skills/pipeline-cwl-to-galaxy/_assembly.json # casts/claude/skills/pipeline-interview-to-galaxy/SKILL.md # casts/claude/skills/pipeline-interview-to-galaxy/_assembly.json # casts/claude/skills/pipeline-nextflow-to-cwl/SKILL.md # casts/claude/skills/pipeline-nextflow-to-cwl/_assembly.json # casts/claude/skills/pipeline-nextflow-to-galaxy/SKILL.md # casts/claude/skills/pipeline-nextflow-to-galaxy/_assembly.json # casts/claude/skills/pipeline-paper-to-cwl/SKILL.md # casts/claude/skills/pipeline-paper-to-cwl/_assembly.json # casts/claude/skills/pipeline-paper-to-galaxy/SKILL.md # casts/claude/skills/pipeline-paper-to-galaxy/_assembly.json # casts/claude/skills/summarize-galaxy-tool/SKILL.md # casts/claude/skills/summarize-galaxy-tool/_provenance.json # casts/claude/skills/summarize-galaxy-tool/_required_tools.json # casts/claude/skills/summarize-galaxy-tool/references/cli/galaxy-tool-cache.md # content/cli/galaxy-tool-cache/index.md # content/cli/gxwf/index.md
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Started from foundry#323 (whose root-cause diagnosis was wrong — stock tools resolve against the Tool Shed by bare id, not a Galaxy instance; the real bug was client-side, fixed upstream in galaxy-tool-util-ts#136 and released in
@galaxy-tool-util/cli1.8.1). This branch fixes the Foundry side and removes the duplication that let the CLI docs drift from the tool.What changed
1. CLI reference pages corrected (
a74657a)galaxy-tool-cache/{add,summarize}.md: bare/stock ids resolve against the shed;--galaxy-urlreframed from "fallback" → "alternate source, tried after the ToolShed"; stock ids need an explicit--tool-version(shed TRS version-list 500s, no auto-version).list.md(cache version-confirmation surface).@galaxy-tool-util/cli@1.8.1runs.2. Built-in/stock branch in the per-step loop Molds (
e8124f9)summarize-galaxy-tool: accepts a bare/stock id; wires[[list]]; documents the bare-idadd/summarizeflow.advance-galaxy-draft-step(step 2): built-in/stock ids skipdiscover-shed-tool/authorand only resolve a version via the cache flow.implement-galaxy-tool-step(steps 2, 4): take stocktool_versionfrom the summary's cached pin; never invent it — closes the hallucinated-version failure in galaxy-tool-cache add fails on stock/built-in tool ids (blocks version lookup in per-step loop) #323.3. Pin
@galaxy-tool-util/clito^1.8.1(770df68)package.json(root +site/); pingxwf/index.mdfor parity withgalaxy-tool-cache. Bumping the dep pulled the corrected stock-tool descriptions into@galaxy-tool-util/cli/metaautomatically.4. De-duplicate CLI flag docs over the node package (
8d6e79c)buildCliSidecarnow embedsdescription/synopsis/args/optionsfrom the package'smetasubpath (the same spec the commander program and--helpare built from) — the single source the site'scli-registryalready renders from. Falls back to body-only for non-meta packages (planemo).galaxy-tool-cachenotes drop their hand-authored## Flagsmirrors;gxwf/draft-validatekeeps its section (genuine--concretebehavioral doc). Adds a cast regression test.Verification
npm run validate(0 errors),npm run test(135 passed),cast --checkclean across the three re-cast Molds, pipeline harnesses re-assembled. CLI bumped 1.7.2 → 1.8.1;@galaxy-tool-util/schemaleft at 1.7.2 to avoid unrelated cast churn.Related
--help/spec descriptions for stock tools (shipped in 1.8.1).gxwf draft-validate --concreteshould resolve built-in versions so a guessed stock version can't validate green.🤖 Generated with Claude Code