Close out #322 residue: renderInstallCommand pin handling + planemo 0.75.45

casts/claude/skills/convert-nfcore-module-to-galaxy-tool/SKILL.md

@@ -21,8 +21,8 @@ Follow the procedure below and use the artifact/reference sections as the runtim
 
 ## Required Tools
 
-- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
-  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
+- **`planemo`** (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`.

casts/claude/skills/convert-nfcore-module-to-galaxy-tool/_provenance.json

@@ -6,16 +6,21 @@
     "path": "content/molds/convert-nfcore-module-to-galaxy-tool/index.md",
     "revision": 4,
     "content_hash": "b620de36e245302737d9a82171fb2847ee214466915dbb28392a0ac02bc6df68",
-    "commit": "dca2ac888332ee86d0cdcb5aabef94804fa16c54"
+    "commit": "39555fca3fd95bf7db8b0191e97135ce20c77cb2"
   },
-  "cast_at": "2026-07-20T16:07:57.008Z",
-  "cast_date": "2026-06-19",
-  "cast_revision": 1,
+  "cast_at": "2026-07-20T18:41:11.132Z",
+  "cast_date": "2026-07-20",
+  "cast_revision": 2,
   "cast_history": [
     {
       "rev": 1,
       "date": "2026-06-19",
       "note": "condense→verbatim; planemo 0.75.44 (fork retired)"
+    },
+    {
+      "rev": 2,
+      "date": "2026-07-20",
+      "note": "planemo 0.75.45"
     }
   ],
   "refs": [
@@ -31,7 +36,7 @@
       "purpose": "Reference for `planemo lint` flags and output classification; first gate in the convergence loop.",
       "trigger": "Step 10.1 — after every <command>/<inputs>/<outputs> emission.",
       "verification": "Cast and confirm the cast skill consults the manpage's exit-code and error-shape sections, not free-text guesses.",
-      "src_hash": "0bdc37ac4d67d672ee7245e5e98323d157ab106efe41b609eef1a08067febbc2",
+      "src_hash": "658bedace8f94b4f88299ecf60b542f670a892c634d2bb602546aae50d7dc5a4",
       "dst_hash": "862d714fa6eb7d9233173948162ff880262e2c867394f1157d073a4ce8d81523",
       "source": "deterministic"
     },
@@ -47,8 +52,8 @@
       "purpose": "Reference for `planemo test --test_output_json` invocation, exit codes, and the JSON report path.",
       "trigger": "Step 10.2 — after lint clears.",
       "verification": "Cast and confirm the cast skill always runs with --test_output_json and reads from the JSON, not stdout.",
-      "src_hash": "4482cb70268a92da6015d90ed4f40c60085f94a649621a052025427607b7472e",
-      "dst_hash": "26b912fe63d0664841cd597437a221eee048e5098affada786a847e265ba1106",
+      "src_hash": "708692af91e36e4bf5b317509df8dee19e4e15617aeaa53a7ddcbfde18b41f74",
+      "dst_hash": "f4698abd6b129048befaa3e335010d99c2748a3a4a5334b90584ce5b9ee913e6",
       "source": "deterministic"
     },
     {
@@ -63,8 +68,8 @@
       "purpose": "Install metadata for the planemo CLI invoked by the convergence loop.",
       "trigger": "Always — the cast skill needs planemo on PATH before running lint/test.",
       "verification": "Cast and confirm the bundle's _required_tools.json carries the pinned planemo install command.",
-      "src_hash": "ffd4938907b27307e05fb6b44a76a29c2a111e5b51072ec51442b17865cfffaf",
-      "dst_hash": "ffd4938907b27307e05fb6b44a76a29c2a111e5b51072ec51442b17865cfffaf",
+      "src_hash": "0f6cee85c6f90b44e33e0b1e1343648be1058084487a55b037c718f3c036ef4b",
+      "dst_hash": "0f6cee85c6f90b44e33e0b1e1343648be1058084487a55b037c718f3c036ef4b",
       "source": "deterministic"
     },
     {

casts/claude/skills/convert-nfcore-module-to-galaxy-tool/_required_tools.json

@@ -3,9 +3,9 @@
     "tool": "planemo",
     "origin": "pypi",
     "package": "planemo",
-    "package_version": "0.75.44",
+    "package_version": "0.75.45",
     "invoke": "planemo",
-    "invoke_fallback": "uvx --from planemo==0.75.44 planemo",
+    "invoke_fallback": "uvx --from planemo==0.75.45 planemo",
     "availability_check": "planemo --version",
     "docs_url": "https://planemo.readthedocs.io/",
     "reference": "references/cli/planemo.md",

casts/claude/skills/convert-nfcore-module-to-galaxy-tool/references/cli/planemo.md

@@ -3,18 +3,18 @@ type: cli-tool
 tool: planemo
 origin: pypi
 package: planemo
-package_version: "0.75.44"
+package_version: "0.75.45"
 invoke: planemo
-invoke_fallback: "uvx --from planemo==0.75.44 planemo"
+invoke_fallback: "uvx --from planemo==0.75.45 planemo"
 availability_check: "planemo --version"
 docs_url: "https://planemo.readthedocs.io/"
 tags:
   - cli-tool
   - cli/planemo
 status: draft
 created: 2026-05-10
-revised: 2026-06-18
-revision: 4
+revised: 2026-07-20
+revision: 5
 ai_generated: true
 summary: "Galaxy tool/workflow runtime testing CLI; used by run-workflow-test and friends."
 ---
@@ -25,20 +25,20 @@ Galaxy's runtime testing and authoring CLI. Foundry Molds invoke `planemo test`,
 
 ## Pin
 
-`package_version` pins to the released `planemo==0.75.44` from PyPI — base upstream planemo, no fork.
+`package_version` pins to the released `planemo==0.75.45` from PyPI — base upstream planemo, no fork.
 
-Released 0.75.44 carries the merged [galaxyproject/planemo#1636](https://github.com/galaxyproject/planemo/pull/1636), so `planemo cli_metadata` and `planemo output_schema` ship in the base release. Every Foundry consumer now runs off this base pin: the workflow-test phases ([[run-workflow-test]], [[implement-galaxy-workflow-test]]) which need only `planemo test --test_output_json`, the convergence loop in [[convert-nfcore-module-to-galaxy-tool]], and the vendored-artifact regeneration story (`packages/planemo-cli-meta/`, `packages/planemo-test-report-schema/`). No fork pin is required.
+[galaxyproject/planemo#1636](https://github.com/galaxyproject/planemo/pull/1636) merged 2026-05-14 and first shipped in released **0.75.42**, so `planemo cli_metadata` and `planemo output_schema` are available in every release at or above this pin. Every Foundry consumer runs off this base pin: the workflow-test phases ([[run-workflow-test]], [[implement-galaxy-workflow-test]]) which need only `planemo test --test_output_json`, the convergence loop in [[convert-nfcore-module-to-galaxy-tool]], and the vendored-artifact regeneration story (`packages/planemo-cli-meta/`, `packages/planemo-test-report-schema/`). No fork pin is required.
 
 ## Install
 
 ```sh
-uvx --from planemo==0.75.44 planemo --version
+uvx --from planemo==0.75.45 planemo --version
 ```
 
 For a persistent install:
 
 ```sh
-uv tool install planemo==0.75.44
+uv tool install planemo==0.75.45
 ```
 
 Contributor laptops only need planemo when **regenerating** vendored artifacts (the schema JSON in `packages/planemo-test-report-schema/`, the planemo CLI manual pages under `content/cli/planemo/`). Normal Foundry development — `npm run validate`, `npm run test`, `npm run packages-test` — builds against the vendored JSON and does not invoke planemo.

casts/claude/skills/implement-galaxy-workflow-test/SKILL.md

@@ -15,20 +15,20 @@ Follow the procedure below and use the artifact/reference sections as the runtim
 
 - Read artifact `galaxy-test-plan`. Schema: galaxy-workflow-test-plan. Produced by `changeset-to-galaxy-test-plan`, `cwl-test-to-galaxy-test-plan`, `freeform-summary-to-galaxy-test-plan`, `nextflow-test-to-galaxy-test-plan`. Schema-valid Galaxy test plan (galaxy-workflow-test-plan) from a *-test-to-galaxy-test-plan Mold; carries job inputs, expected outputs, assertion intent, fixture provenance, label assumptions, unresolved mappings, and omissions.
 - Read artifact `galaxy-workflow`. Produced by `advance-galaxy-draft-step`. Concrete gxformat2 workflow being tested — the loop-endstate `galaxy-workflow.gxwf.yml` from advance-galaxy-draft-step (`class: GalaxyWorkflow`); provides the real input/output labels, outputs, and collection shapes the test must assert against.
-- Read artifact `test-data-refs`. Produced by `find-test-data`, `paper-to-test-data`. Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.
+- Read artifact `test-data-refs`. Produced by `cwl-to-test-data`, `find-test-data`, `nextflow-to-test-data`, `paper-to-test-data`. Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.
 
 ## Outputs
 
 - Write artifact `galaxy-workflow-test` as `galaxy-workflow.gxwf-tests.yml`. Format: `yaml`. Galaxy workflow test file (tests-format) with job inputs, expected outputs, assertions; passes static schema + label cross-check. Named as the workflow basename + `-tests.yml` so Planemo discovers it as the companion of `galaxy-workflow.gxwf.yml`.
 
 ## Required Tools
 
-- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
+- **`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/cli
-- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
-  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
+- **`planemo`** (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`.

casts/claude/skills/implement-galaxy-workflow-test/_provenance.json

@@ -6,9 +6,18 @@
     "path": "content/molds/implement-galaxy-workflow-test/index.md",
     "revision": 7,
     "content_hash": "7f68fe27b39a85abaf6c15f1647809b0d28c71753a7de463a52ffcd5e440f82a",
-    "commit": "2e8ea5a6363235576bacfa5defd11492bbab6f94"
+    "commit": "39555fca3fd95bf7db8b0191e97135ce20c77cb2"
   },
-  "cast_at": "2026-07-10T18:51:40.524Z",
+  "cast_at": "2026-07-20T18:41:10.395Z",
+  "cast_date": "2026-07-20",
+  "cast_revision": 1,
+  "cast_history": [
+    {
+      "rev": 1,
+      "date": "2026-07-20",
+      "note": "planemo 0.75.45"
+    }
+  ],
   "refs": [
     {
       "kind": "cli-command",
@@ -35,8 +44,8 @@
       "load": "upfront",
       "evidence": "corpus-observed",
       "purpose": "Runtime for workflow_test_init / workflow_test_on_invocation; install before authoring tests against a live invocation.",
-      "src_hash": "ffd4938907b27307e05fb6b44a76a29c2a111e5b51072ec51442b17865cfffaf",
-      "dst_hash": "ffd4938907b27307e05fb6b44a76a29c2a111e5b51072ec51442b17865cfffaf",
+      "src_hash": "0f6cee85c6f90b44e33e0b1e1343648be1058084487a55b037c718f3c036ef4b",
+      "dst_hash": "0f6cee85c6f90b44e33e0b1e1343648be1058084487a55b037c718f3c036ef4b",
       "source": "deterministic"
     },
     {
@@ -180,7 +189,9 @@
         "id": "test-data-refs",
         "description": "Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.",
         "producers": [
+          "cwl-to-test-data",
           "find-test-data",
+          "nextflow-to-test-data",
           "paper-to-test-data"
         ]
       }

casts/claude/skills/implement-galaxy-workflow-test/_required_tools.json

@@ -17,9 +17,9 @@
     "tool": "planemo",
     "origin": "pypi",
     "package": "planemo",
-    "package_version": "0.75.44",
+    "package_version": "0.75.45",
     "invoke": "planemo",
-    "invoke_fallback": "uvx --from planemo==0.75.44 planemo",
+    "invoke_fallback": "uvx --from planemo==0.75.45 planemo",
     "availability_check": "planemo --version",
     "docs_url": "https://planemo.readthedocs.io/",
     "reference": "references/cli/planemo.md",

casts/claude/skills/implement-galaxy-workflow-test/references/cli/planemo.md

@@ -3,18 +3,18 @@ type: cli-tool
 tool: planemo
 origin: pypi
 package: planemo
-package_version: "0.75.44"
+package_version: "0.75.45"
 invoke: planemo
-invoke_fallback: "uvx --from planemo==0.75.44 planemo"
+invoke_fallback: "uvx --from planemo==0.75.45 planemo"
 availability_check: "planemo --version"
 docs_url: "https://planemo.readthedocs.io/"
 tags:
   - cli-tool
   - cli/planemo
 status: draft
 created: 2026-05-10
-revised: 2026-06-18
-revision: 4
+revised: 2026-07-20
+revision: 5
 ai_generated: true
 summary: "Galaxy tool/workflow runtime testing CLI; used by run-workflow-test and friends."
 ---
@@ -25,20 +25,20 @@ Galaxy's runtime testing and authoring CLI. Foundry Molds invoke `planemo test`,
 
 ## Pin
 
-`package_version` pins to the released `planemo==0.75.44` from PyPI — base upstream planemo, no fork.
+`package_version` pins to the released `planemo==0.75.45` from PyPI — base upstream planemo, no fork.
 
-Released 0.75.44 carries the merged [galaxyproject/planemo#1636](https://github.com/galaxyproject/planemo/pull/1636), so `planemo cli_metadata` and `planemo output_schema` ship in the base release. Every Foundry consumer now runs off this base pin: the workflow-test phases ([[run-workflow-test]], [[implement-galaxy-workflow-test]]) which need only `planemo test --test_output_json`, the convergence loop in [[convert-nfcore-module-to-galaxy-tool]], and the vendored-artifact regeneration story (`packages/planemo-cli-meta/`, `packages/planemo-test-report-schema/`). No fork pin is required.
+[galaxyproject/planemo#1636](https://github.com/galaxyproject/planemo/pull/1636) merged 2026-05-14 and first shipped in released **0.75.42**, so `planemo cli_metadata` and `planemo output_schema` are available in every release at or above this pin. Every Foundry consumer runs off this base pin: the workflow-test phases ([[run-workflow-test]], [[implement-galaxy-workflow-test]]) which need only `planemo test --test_output_json`, the convergence loop in [[convert-nfcore-module-to-galaxy-tool]], and the vendored-artifact regeneration story (`packages/planemo-cli-meta/`, `packages/planemo-test-report-schema/`). No fork pin is required.
 
 ## Install
 
 ```sh
-uvx --from planemo==0.75.44 planemo --version
+uvx --from planemo==0.75.45 planemo --version
 ```
 
 For a persistent install:
 
 ```sh
-uv tool install planemo==0.75.44
+uv tool install planemo==0.75.45
 ```
 
 Contributor laptops only need planemo when **regenerating** vendored artifacts (the schema JSON in `packages/planemo-test-report-schema/`, the planemo CLI manual pages under `content/cli/planemo/`). Normal Foundry development — `npm run validate`, `npm run test`, `npm run packages-test` — builds against the vendored JSON and does not invoke planemo.

casts/claude/skills/pipeline-cwl-to-galaxy/SKILL.md

@@ -27,12 +27,12 @@ Install the harness CLIs every constituent skill invokes before driving the pipe
   Ephemeral run: `npx --package @galaxy-foundry/foundry foundry`.
   Check: `foundry --help`.
   Docs: https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md
-- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
+- **`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/cli
-- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
-  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
+- **`planemo`** (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/
 

casts/claude/skills/pipeline-cwl-to-galaxy/_assembly.json

@@ -8,7 +8,7 @@
     { "tool": "cwltool", "origin": "pypi", "package": "cwltool", "invoke": "cwltool", "invoke_fallback": "uvx cwltool", "availability_check": "cwltool --version", "docs_url": "https://cwltool.readthedocs.io/", "source": "referenced" },
     { "tool": "foundry", "origin": "npm", "package": "@galaxy-foundry/foundry", "invoke": "foundry", "invoke_fallback": "npx --package @galaxy-foundry/foundry foundry", "availability_check": "foundry --help", "docs_url": "https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md", "source": "referenced" },
     { "tool": "gxwf", "origin": "npm", "package": "@galaxy-tool-util/cli", "package_version": "^1.8.1", "invoke": "gxwf", "invoke_fallback": "npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf", "availability_check": "gxwf --help | grep -q draft-validate", "docs_url": "https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli", "source": "implied", "implied_by": ["gxwf convert", "gxwf draft-validate", "gxwf draft-next-step", "gxwf draft-extract", "gxwf validate-tests", "gxwf validate"] },
-    { "tool": "planemo", "origin": "pypi", "package": "planemo", "package_version": "0.75.44", "invoke": "planemo", "invoke_fallback": "uvx --from planemo==0.75.44 planemo", "availability_check": "planemo --version", "docs_url": "https://planemo.readthedocs.io/", "source": "referenced" }
+    { "tool": "planemo", "origin": "pypi", "package": "planemo", "package_version": "0.75.45", "invoke": "planemo", "invoke_fallback": "uvx --from planemo==0.75.45 planemo", "availability_check": "planemo --version", "docs_url": "https://planemo.readthedocs.io/", "source": "referenced" }
   ],
   "phases": [
     { "phase": 1, "kind": "mold", "skill": "summarize-cwl", "cast_present": true, "loop": false },

casts/claude/skills/pipeline-interview-to-galaxy/SKILL.md

@@ -15,12 +15,12 @@ Harness for the **INTERVIEW → GALAXY** Foundry pipeline. Runs the constituent
 
 Install the harness CLIs every constituent skill invokes before driving the pipeline. Deduped across all phases; bioinformatics tools the constructed workflow installs are out of scope (the discovery phase pins those).
 
-- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
+- **`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/cli
-- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
-  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
+- **`planemo`** (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/
 

casts/claude/skills/pipeline-interview-to-galaxy/_assembly.json

@@ -5,7 +5,7 @@
   "options": ["use-subagents", "checkpoint"],
   "required_tools": [
     { "tool": "gxwf", "origin": "npm", "package": "@galaxy-tool-util/cli", "package_version": "^1.8.1", "invoke": "gxwf", "invoke_fallback": "npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf", "availability_check": "gxwf --help | grep -q draft-validate", "docs_url": "https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli", "source": "implied", "implied_by": ["gxwf convert", "gxwf draft-validate", "gxwf draft-next-step", "gxwf draft-extract", "gxwf validate-tests", "gxwf validate"] },
-    { "tool": "planemo", "origin": "pypi", "package": "planemo", "package_version": "0.75.44", "invoke": "planemo", "invoke_fallback": "uvx --from planemo==0.75.44 planemo", "availability_check": "planemo --version", "docs_url": "https://planemo.readthedocs.io/", "source": "referenced" }
+    { "tool": "planemo", "origin": "pypi", "package": "planemo", "package_version": "0.75.45", "invoke": "planemo", "invoke_fallback": "uvx --from planemo==0.75.45 planemo", "availability_check": "planemo --version", "docs_url": "https://planemo.readthedocs.io/", "source": "referenced" }
   ],
   "phases": [
     { "phase": 1, "kind": "mold", "skill": "interview-to-freeform-summary", "cast_present": true, "loop": false },

casts/claude/skills/pipeline-nextflow-to-cwl/SKILL.md

@@ -21,12 +21,12 @@ Install the harness CLIs every constituent skill invokes before driving the pipe
   Ephemeral run: `npx --package @galaxy-foundry/foundry foundry`.
   Check: `foundry --help`.
   Docs: https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md
-- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
+- **`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/cli
-- **`planemo`** (planemo). `uv tool install planemo==0.75.44` (or `pip install planemo==0.75.44`).
-  Ephemeral run: `uvx --from planemo==0.75.44 planemo`.
+- **`planemo`** (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/