@galaxy-tool-util/schema 1.10.1 → 1.13.1

package/dist/user-tool-parse/inputs.js.map

@@ -1 +1 @@
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package/dist/user-tool-parse/outputs.d.ts

@@ -5,6 +5,7 @@
  * Produces the `ToolOutput` union from `../schema/parsed-tool.ts` (data /
  * collection / text / integer / float / boolean).
  */
-import type { ToolOutput } from "../schema/parsed-tool.js";
+import type { DatasetCollectionDescription, ToolOutput } from "../schema/parsed-tool.js";
 export declare function parseOutputs(raw: unknown): ToolOutput[];
+export declare function parseDiscoverDatasets(raw: unknown): DatasetCollectionDescription[] | null;
 //# sourceMappingURL=outputs.d.ts.map

package/dist/user-tool-parse/outputs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"outputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/outputs.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAGV,UAAU,EAOX,MAAM,0BAA0B,CAAC;AAwBlC,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,UAAU,EAAE,CAGvD"}
+{"version":3,"file":"outputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/outputs.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EACV,4BAA4B,EAE5B,UAAU,EAOX,MAAM,0BAA0B,CAAC;AAwBlC,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,UAAU,EAAE,CAGvD;AAuFD,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,OAAO,GAAG,4BAA4B,EAAE,GAAG,IAAI,CAezF"}

package/dist/user-tool-parse/outputs.js

@@ -87,7 +87,7 @@ function parseOutputCollection(entry) {
         label: readNullableString(entry.label),
         hidden: readBool(entry.hidden, false),
         type: "collection",
-        structure: parseStructure(entry),
+        ...parseStructure(entry),
     };
 }
 function parseStructure(entry) {
@@ -109,7 +109,7 @@ function parseStructure(entry) {
         discover_datasets: discoverDatasets,
     };
 }
-function parseDiscoverDatasets(raw) {
+export function parseDiscoverDatasets(raw) {
     let list;
     if (raw === undefined || raw === null)
         return null;
@@ -135,7 +135,8 @@ function parseDiscoverDataset(entry) {
             ? "tool_provided_metadata"
             : "pattern";
     const base = {
-        format: readNullableString(entry.format ?? entry.ext),
+        // ext-first, matching Galaxy's DatasetCollectionDescription (ext, then format).
+        format: readNullableString(entry.ext ?? entry.format),
         visible: readBool(entry.visible, false),
         assign_primary_output: readBool(entry.assign_primary_output, false),
         directory: readNullableString(entry.directory),

package/dist/user-tool-parse/outputs.js.map

@@ -1 +1 @@
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package/dist/user-tool-parse/parse.d.ts

@@ -1,12 +1,27 @@
 /**
- * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * YAML tool → ParsedTool conversion. Mirrors
  * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
  * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
  * for the parameter / output trees.
  */
 import type { ParsedTool } from "../schema/parsed-tool.js";
-export type InlineRepresentation = Record<string, unknown>;
+/** A decoded YAML tool document (`class: GalaxyTool` or `GalaxyUserTool`). */
+export type YamlToolRepresentation = Record<string, unknown>;
+/** The inline-tool API's `tool_representation` (always `class: GalaxyUserTool`). */
+export type InlineRepresentation = YamlToolRepresentation;
 export declare class InlineToolParseError extends Error {
 }
+/**
+ * Parse a decoded YAML tool document into a `ParsedTool`. Handles both the
+ * legacy `GalaxyTool` and the user-facing `GalaxyUserTool` classes — the input
+ * and output trees already cover the block/when-map inputs and map-form outputs
+ * the `GalaxyTool` format uses, so a single field layout serves both.
+ */
+export declare function parseYamlTool(repr: YamlToolRepresentation): ParsedTool;
+/**
+ * Parse an inline `GalaxyUserTool` representation. Enforces the `GalaxyUserTool`
+ * class the inline-tool API contract requires, then delegates to
+ * {@link parseYamlTool}.
+ */
 export declare function parseInlineTool(repr: InlineRepresentation): ParsedTool;
 //# sourceMappingURL=parse.d.ts.map

package/dist/user-tool-parse/parse.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/parse.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAmC,MAAM,0BAA0B,CAAC;AAK5F,8EAA8E;AAC9E,MAAM,MAAM,sBAAsB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE7D,oFAAoF;AACpF,MAAM,MAAM,oBAAoB,GAAG,sBAAsB,CAAC;AAE1D,qBAAa,oBAAqB,SAAQ,KAAK;CAAG;AAElD;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,sBAAsB,GAAG,UAAU,CAyBtE;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,oBAAoB,GAAG,UAAU,CAUtE"}

package/dist/user-tool-parse/parse.js

@@ -1,5 +1,5 @@
 /**
- * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * YAML tool → ParsedTool conversion. Mirrors
  * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
  * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
  * for the parameter / output trees.
@@ -8,12 +8,15 @@ import { parseInputs } from "./inputs.js";
 import { parseOutputs } from "./outputs.js";
 export class InlineToolParseError extends Error {
 }
-export function parseInlineTool(repr) {
+/**
+ * Parse a decoded YAML tool document into a `ParsedTool`. Handles both the
+ * legacy `GalaxyTool` and the user-facing `GalaxyUserTool` classes — the input
+ * and output trees already cover the block/when-map inputs and map-form outputs
+ * the `GalaxyTool` format uses, so a single field layout serves both.
+ */
+export function parseYamlTool(repr) {
     if (!repr || typeof repr !== "object" || Array.isArray(repr)) {
-        throw new InlineToolParseError("inline tool representation must be an object");
-    }
-    if (repr.class !== "GalaxyUserTool") {
-        throw new InlineToolParseError(`inline tool representation must have class 'GalaxyUserTool' (got ${JSON.stringify(repr.class)})`);
+        throw new InlineToolParseError("tool representation must be an object");
     }
     const id = typeof repr.id === "string" ? repr.id : "";
     const version = repr.version == null ? null : String(repr.version);
@@ -35,6 +38,20 @@ export function parseInlineTool(repr) {
         help: parseHelp(repr.help),
     };
 }
+/**
+ * Parse an inline `GalaxyUserTool` representation. Enforces the `GalaxyUserTool`
+ * class the inline-tool API contract requires, then delegates to
+ * {@link parseYamlTool}.
+ */
+export function parseInlineTool(repr) {
+    if (!repr || typeof repr !== "object" || Array.isArray(repr)) {
+        throw new InlineToolParseError("inline tool representation must be an object");
+    }
+    if (repr.class !== "GalaxyUserTool") {
+        throw new InlineToolParseError(`inline tool representation must have class 'GalaxyUserTool' (got ${JSON.stringify(repr.class)})`);
+    }
+    return parseYamlTool(repr);
+}
 function parseStringList(raw) {
     if (!Array.isArray(raw))
         return [];

package/dist/user-tool-parse/parse.js.map

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+{"version":3,"file":"parse.js","sourceRoot":"","sources":["../../src/user-tool-parse/parse.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC1C,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAQ5C,MAAM,OAAO,oBAAqB,SAAQ,KAAK;CAAG;AAElD;;;;;GAKG;AACH,MAAM,UAAU,aAAa,CAAC,IAA4B;IACxD,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7D,MAAM,IAAI,oBAAoB,CAAC,uCAAuC,CAAC,CAAC;IAC1E,CAAC;IAED,MAAM,EAAE,GAAG,OAAO,IAAI,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;IACtD,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACnE,MAAM,IAAI,GAAG,CAAC,OAAO,IAAI,CAAC,IAAI,KAAK,QAAQ,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC;IACtE,MAAM,WAAW,GAAG,OAAO,IAAI,CAAC,WAAW,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC;IAEjF,OAAO;QACL,EAAE;QACF,OAAO;QACP,IAAI;QACJ,WAAW,EAAE,WAAW,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW;QACpD,MAAM,EAAE,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;QAChC,OAAO,EAAE,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC;QACnC,SAAS,EAAE,cAAc,CAAC,IAAI,CAAC,SAAS,CAAC;QACzC,OAAO,EAAE,OAAO,IAAI,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI;QAC/D,OAAO,EAAE,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC;QACnC,eAAe,EAAE,eAAe,CAAC,IAAI,CAAC,eAAe,CAAC;QACtD,WAAW,EAAE,eAAe,CAAC,IAAI,CAAC,WAAW,CAAC;QAC9C,KAAK,EAAE,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC;QAC7B,IAAI,EAAE,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC;KAC3B,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAAC,IAA0B;IACxD,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7D,MAAM,IAAI,oBAAoB,CAAC,8CAA8C,CAAC,CAAC;IACjF,CAAC;IACD,IAAI,IAAI,CAAC,KAAK,KAAK,gBAAgB,EAAE,CAAC;QACpC,MAAM,IAAI,oBAAoB,CAC5B,oEAAoE,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAClG,CAAC;IACJ,CAAC;IACD,OAAO,aAAa,CAAC,IAAI,CAAC,CAAC;AAC7B,CAAC;AAED,SAAS,eAAe,CAAC,GAAY;IACnC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IACnC,OAAO,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,OAAO,CAAC,KAAK,QAAQ,CAAC,CAAC;AAC/D,CAAC;AAED,SAAS,YAAY,CAAC,GAAY;IAChC,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,GAAG;QAAE,OAAO,GAAG,CAAC;IAC/C,IAAI,OAAO,GAAG,KAAK,QAAQ;QAAE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC;IAChD,kDAAkD;IAClD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,cAAc,CAAC,GAAY;IAClC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IACnC,MAAM,GAAG,GAAe,EAAE,CAAC;IAC3B,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;QACxB,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;YAAE,SAAS;QAClD,MAAM,CAAC,GAAG,KAAgC,CAAC;QAC3C,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC;QACxD,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;QACjE,IAAI,IAAI,IAAI,OAAO,KAAK,IAAI;YAAE,GAAG,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC;IAC5D,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,SAAS,UAAU,CAAC,GAAY;IAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IACnC,MAAM,GAAG,GAAe,EAAE,CAAC;IAC3B,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;QACxB,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;YAAE,SAAS;QAClD,MAAM,CAAC,GAAG,KAAgC,CAAC;QAC3C,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC;QAC3D,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC;QACxD,iEAAiE;QACjE,IAAI,KAAK,KAAK,IAAI,IAAI,IAAI;YAAE,GAAG,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;IACxD,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,SAAS,SAAS,CAAC,GAAY;IAC7B,IAAI,GAAG,IAAI,IAAI;QAAE,OAAO,IAAI,CAAC;IAC7B,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;QAC5B,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;IAC9C,CAAC;IACD,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QACnD,MAAM,CAAC,GAAG,GAA8B,CAAC;QACzC,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;QACjE,IAAI,OAAO,KAAK,IAAI;YAAE,OAAO,IAAI,CAAC;QAClC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC;QACpE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC;IAC7B,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/dist/workflow/cytoscape.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cytoscape.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAEV,iBAAiB,EAIlB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,yBAAyB,CAAC;AASjC,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB;;;;;;;OAOG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AAED,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,gBAAqB,GAC1B,iBAAiB,CAuEnB"}
+{"version":3,"file":"cytoscape.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAEV,iBAAiB,EAIlB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,yBAAyB,CAAC;AAUjC,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB;;;;;;;OAOG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AAED,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,gBAAqB,GAC1B,iBAAiB,CAuEnB"}

package/dist/workflow/cytoscape.js

@@ -9,6 +9,7 @@ import { bakesCoordinates, topologicalPositions } from "./cytoscape-layout.js";
 import { isDraftWorkflow, isTodoSentinel, PLANNED_CLASS, resolveDraftOverlay, } from "./draft-checks.js";
 import { edgeAnnotationKey } from "./edge-annotation.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
+import { isGalaxyUserToolRun } from "./normalized/format2.js";
 import { isUnlabeledStep, resolveSourceReference, stepRenderIdentity, } from "./normalized/labels.js";
 const MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/";
 export function cytoscapeElements(workflow, opts = {}) {
@@ -117,9 +118,10 @@ function _inputNode(inp, orderIndex) {
 }
 function _stepNode(step, orderIndex, overlay) {
     const stepId = stepRenderIdentity(step);
-    // The TS normalizer doesn't infer step.type the way gxformat2 does, so fall
-    // back to a `run`-derived hint for subworkflows (matches mermaid emitter).
-    const stepType = step.type || (step.run != null ? "subworkflow" : "tool");
+    // An embedded GalaxyUserTool run is a tool, while workflow runs are subworkflows.
+    const stepType = isGalaxyUserToolRun(step.run)
+        ? "tool"
+        : step.type || (step.run != null ? "subworkflow" : "tool");
     let strippedToolId = step.tool_id ?? null;
     if (strippedToolId && strippedToolId.startsWith(MAIN_TS_PREFIX)) {
         strippedToolId = strippedToolId.slice(MAIN_TS_PREFIX.length);

package/dist/workflow/cytoscape.js.map

@@ -1 +1 @@
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package/dist/workflow/draft-checks.d.ts

@@ -120,7 +120,8 @@ export interface DraftValidationResult {
  *                    input labels, output labels, step labels, and step types
  *                    cannot be TODO sentinels. Step/port edge refs must
  *                    resolve to a declared step + declared port (TODO_*
- *                    ports count if declared in the step's `out:`).
+ *                    ports count if declared in the step's `out:`; an
+ *                    embedded `GalaxyUserTool` also declares its outputs).
  *   semanticErrors   TODO-shaped strings (start with `TODO`) that don't
  *                    match the canonical sentinel form (e.g. `TODO-foo`,
  *                    `TODOfoo`, `TODO_` trailing).

package/dist/workflow/draft-checks.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/draft-checks.js

@@ -11,6 +11,7 @@
 import { Either, ParseResult, Schema } from "effect";
 import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
 import { rawStepRenderIdentity, resolveSourceReference } from "./normalized/labels.js";
+import { isGalaxyUserToolRun } from "./normalized/format2.js";
 export const TODO_SENTINEL_PATTERN = /^TODO(_[a-zA-Z0-9_]+)?$/;
 // Heuristic for TODO-shaped strings — flags malformed sentinels (TODO-foo,
 // TODOfoo, TODO_) that the canonical pattern misses. Mixed-case suffixes
@@ -250,6 +251,28 @@ function* iterateStepOutIds(out) {
         }
     }
 }
+/**
+ * Output ports a step exposes: its declared `out:` ids, plus every output an
+ * embedded `GalaxyUserTool` run defines — Galaxy creates those whether or not
+ * `out:` lists them.
+ */
+function stepOutPorts(step) {
+    const ports = new Set(iterateStepOutIds(step.out));
+    if (isGalaxyUserToolRun(step.run)) {
+        const outputs = step.run.outputs;
+        if (Array.isArray(outputs)) {
+            for (const output of outputs) {
+                if (isRecord(output) && typeof output.name === "string")
+                    ports.add(output.name);
+            }
+        }
+        else if (isRecord(outputs)) {
+            for (const name of Object.keys(outputs))
+                ports.add(name);
+        }
+    }
+    return ports;
+}
 function isRecord(value) {
     return typeof value === "object" && value !== null && !Array.isArray(value);
 }
@@ -261,7 +284,8 @@ function isRecord(value) {
  *                    input labels, output labels, step labels, and step types
  *                    cannot be TODO sentinels. Step/port edge refs must
  *                    resolve to a declared step + declared port (TODO_*
- *                    ports count if declared in the step's `out:`).
+ *                    ports count if declared in the step's `out:`; an
+ *                    embedded `GalaxyUserTool` also declares its outputs).
  *   semanticErrors   TODO-shaped strings (start with `TODO`) that don't
  *                    match the canonical sentinel form (e.g. `TODO-foo`,
  *                    `TODOfoo`, `TODO_` trailing).
@@ -458,8 +482,7 @@ function buildStepIndex(steps) {
     for (const [label, step] of iterateSteps(steps)) {
         if (!isRecord(step))
             continue;
-        const outPorts = new Set(iterateStepOutIds(step.out));
-        index.set(label, { outPorts });
+        index.set(label, { outPorts: stepOutPorts(step) });
     }
     return index;
 }
@@ -864,7 +887,8 @@ function directDropReason(step) {
 }
 /**
  * For each surviving step, compute its currently-live output ports:
- *   - Non-subworkflow steps: all declared `out:` ids.
+ *   - Non-subworkflow steps: all declared `out:` ids, plus the outputs of an
+ *     embedded `GalaxyUserTool` run.
  *   - Inline-draft subworkflow steps: keys of the recursed inner workflow's
  *     surviving outputs (so outer refs that referenced now-dropped inner
  *     outputs evaluate as dead).
@@ -887,7 +911,7 @@ function computeLivePorts(stepEntries, drops, innerResults) {
             livePorts.set(label, surviving);
         }
         else {
-            livePorts.set(label, new Set(iterateStepOutIds(step.out)));
+            livePorts.set(label, stepOutPorts(step));
         }
     }
     return livePorts;