@galaxy-tool-util/schema 1.12.0 → 1.14.0

package/dist/workflow/lint.js.map

@@ -1 +1 @@
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package/dist/workflow/lint_profiles.yml

@@ -10,6 +10,7 @@ structural:
   description: "Checks that prevent execution or indicate structural breakage."
   rules:
     - NativeStepKeyNotInteger
+    - StepLabelNotUnique
     - StepExportError
     - StepUsesTestToolshed
     - WorkflowHasNoOutputs

package/dist/workflow/mermaid.d.ts

@@ -5,7 +5,7 @@
  */
 import type { DraftOverlay } from "./draft-checks.js";
 import type { EdgeAnnotation } from "./edge-annotation.js";
-import type { NormalizedFormat2Workflow } from "./normalized/format2.js";
+import { type NormalizedFormat2Workflow } from "./normalized/format2.js";
 export interface MermaidOptions {
     comments?: boolean;
     /**

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

@@ -1 +1 @@
-{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6BzE,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAuJR"}
+{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAAuB,KAAK,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6B9F,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAwJR"}

package/dist/workflow/mermaid.js

@@ -6,6 +6,7 @@
 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 SHAPE_INPUT = [">", "]"];
 const SHAPE_PARAM = ["{{", "}}"];
@@ -118,9 +119,10 @@ export function workflowToMermaid(workflow, opts = {}) {
         const displayId = step.id && !isUnlabeledStep(step.id) ? step.id : null;
         const rawLabel = step.label || displayId || (toolId ? `tool:${toolId}` : String(i));
         const label = sanitizeLabel(rawLabel);
-        // The TS normalizer does not infer step.type the way gxformat2 does, so
-        // fall back to `run` shape: anything non-null implies a subworkflow.
-        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");
         const shape = STEP_TYPE_SHAPES[stepType] ?? SHAPE_TOOL;
         stepLines.set(stepLabel, nodeLine(nodeId, label, shape));
     });

package/dist/workflow/mermaid.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/expanded.d.ts

@@ -44,6 +44,18 @@ export interface ExpansionOptions {
 export declare const MAX_EXPANSION_DEPTH = 10;
 /** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
 export declare function isTrsUrl(url: string): boolean;
+/**
+ * Build the GA4GH TRS `GALAXY` descriptor URL for a TRS tool version URL.
+ *
+ * The tool id may be percent-encoded or not (Galaxy and planemo emit it
+ * unencoded, e.g. `.../tools/#workflow/github.com/org/repo/main/versions/v1`),
+ * so it is unquoted and re-encoded to keep `#` and `/` from being misread as
+ * URL syntax. Any trailing path (such as `/GALAXY/descriptor`) is ignored.
+ * Returns `null` if `url` is not a TRS URL.
+ *
+ * Port of gxformat2/options.py trs_descriptor_url (mirrors Galaxy's trs_proxy).
+ */
+export declare function trsDescriptorUrl(url: string): string | null;
 /**
  * Normalize and expand a Format2 workflow.
  *

package/dist/workflow/normalized/expanded.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expanded.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,yBAAyB,EAAE,qBAAqB,EAAE,MAAM,cAAc,CAAC;AAErF,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAUlF,MAAM,MAAM,uBAAuB,GAAG,yBAAyB,CAAC;AAChE,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AACxD,MAAM,MAAM,sBAAsB,GAAG,wBAAwB,CAAC;AAC9D,MAAM,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEtD;;;;;;;;GAQG;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAE5E;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,WAAW,CAAC;CACxB;AAID,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAMtC,sEAAsE;AACtE,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE7C;AA8DD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,uBAAuB,CAAC,CAQlC;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAClC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,sBAAsB,CAAC,CAQjC"}
+{"version":3,"file":"expanded.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAEV,yBAAyB,EACzB,qBAAqB,EACtB,MAAM,cAAc,CAAC;AAEtB,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAUlF,MAAM,MAAM,uBAAuB,GAAG,yBAAyB,CAAC;AAChE,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AACxD,MAAM,MAAM,sBAAsB,GAAG,wBAAwB,CAAC;AAC9D,MAAM,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEtD;;;;;;;;GAQG;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAE5E;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,WAAW,CAAC;CACxB;AAID,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAStC,sEAAsE;AACtE,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE7C;AAwBD;;;;;;;;;;GAUG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAQ3D;AA8DD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,uBAAuB,CAAC,CAQlC;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAClC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,sBAAsB,CAAC,CAQjC"}

package/dist/workflow/normalized/expanded.js

@@ -8,18 +8,59 @@
  * Port of gxformat2/normalized/_conversion.py expanded_format2/expanded_native
  * and gxformat2/options.py (UrlResolverFn, default_url_resolver, ConversionOptions).
  */
-import { normalizedFormat2 } from "./format2.js";
+import { isGalaxyUserToolRun, normalizedFormat2 } from "./format2.js";
 import { normalizedNative } from "./native.js";
 import { toFormat2 } from "./toFormat2.js";
 import { toNative } from "./toNative.js";
 // --- Constants ---
 export const MAX_EXPANSION_DEPTH = 10;
-const TRS_URL_REGEX = /^https?:\/\/.+\/ga4gh\/trs\/v2\/tools\/.+\/versions\/[^/]+/;
+const TRS_URL_REGEX = /^(?<trsBaseUrl>https?:\/\/.+)\/ga4gh\/trs\/v2\/tools\/(?<toolId>.+)\/versions\/(?<versionId>[^/]+)/;
+const GA4GH_GALAXY_DESCRIPTOR = "GALAXY";
 // --- Helpers ---
 /** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
 export function isTrsUrl(url) {
     return TRS_URL_REGEX.test(url);
 }
+/**
+ * Percent-decode `%XX` runs (Python's `unquote`). A run that isn't valid UTF-8
+ * is left as-is, so it ends up double-encoded (`%25XX`) where Python would emit
+ * U+FFFD. Real TRS ids are ASCII; parity there isn't worth a TextDecoder.
+ */
+function _unquote(value) {
+    return value.replace(/(?:%[0-9A-Fa-f]{2})+/g, (run) => {
+        try {
+            return decodeURIComponent(run);
+        }
+        catch {
+            return run;
+        }
+    });
+}
+/** Percent-encode like Python's `quote_plus`: only `A-Za-z0-9_.-~` kept, space as `+`. */
+function _quotePlus(value) {
+    return encodeURIComponent(value)
+        .replace(/[!'()*]/g, (c) => `%${c.charCodeAt(0).toString(16).toUpperCase()}`)
+        .replace(/%20/g, "+");
+}
+/**
+ * Build the GA4GH TRS `GALAXY` descriptor URL for a TRS tool version URL.
+ *
+ * The tool id may be percent-encoded or not (Galaxy and planemo emit it
+ * unencoded, e.g. `.../tools/#workflow/github.com/org/repo/main/versions/v1`),
+ * so it is unquoted and re-encoded to keep `#` and `/` from being misread as
+ * URL syntax. Any trailing path (such as `/GALAXY/descriptor`) is ignored.
+ * Returns `null` if `url` is not a TRS URL.
+ *
+ * Port of gxformat2/options.py trs_descriptor_url (mirrors Galaxy's trs_proxy).
+ */
+export function trsDescriptorUrl(url) {
+    const match = TRS_URL_REGEX.exec(url);
+    if (!match?.groups)
+        return null;
+    const { trsBaseUrl, toolId, versionId } = match.groups;
+    return (`${trsBaseUrl}/ga4gh/trs/v2/tools/${_quotePlus(_unquote(toolId))}` +
+        `/versions/${versionId}/${GA4GH_GALAXY_DESCRIPTOR}/descriptor`);
+}
 /** Check if a content_id is a URL that can be fetched. */
 function _isResolvableUrl(contentId) {
     return (contentId.startsWith("http://") ||
@@ -102,6 +143,8 @@ export async function expandedNative(raw, options) {
 // --- Sync expansion (no resolver — inline subworkflows only) ---
 function _expandFormat2Sync(wf) {
     const expandedSteps = wf.steps.map((step) => {
+        if (isGalaxyUserToolRun(step.run))
+            return step;
         if (step.run && typeof step.run === "object") {
             return { ...step, run: _expandFormat2Sync(step.run) };
         }
@@ -126,7 +169,11 @@ async function _expandFormat2(wf, ctx) {
     const expandedSteps = [];
     for (const step of wf.steps) {
         let expandedRun = null;
-        if (step.run && typeof step.run === "object") {
+        if (isGalaxyUserToolRun(step.run)) {
+            // Embedded user-defined tool — nothing to resolve
+            expandedRun = step.run;
+        }
+        else if (step.run && typeof step.run === "object") {
             // Already-inlined subworkflow — recurse
             expandedRun = await _expandFormat2(step.run, ctx);
         }

package/dist/workflow/normalized/expanded.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/format2.d.ts

@@ -32,6 +32,8 @@ export declare const NormalizedFormat2InputSchema: Schema.Struct<{
     type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
     optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
     default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+    min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
+    max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
     format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
     collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
     position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -45,6 +47,18 @@ export declare const NormalizedFormat2OutputSchema: Schema.Struct<{
     type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
 }>;
 export type NormalizedFormat2Output = typeof NormalizedFormat2OutputSchema.Type;
+/**
+ * An embedded user-defined tool under a step's `run:` (`class: GalaxyUserTool`).
+ * Only the discriminator is modelled; the rest of the tool definition passes
+ * through untouched. Mirrors gxformat2's `GalaxyUserToolStub`.
+ */
+export declare const GalaxyUserToolStubSchema: Schema.TypeLiteral<{
+    class: Schema.Literal<["GalaxyUserTool"]>;
+    name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+}, readonly [Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
+export type GalaxyUserToolStub = typeof GalaxyUserToolStubSchema.Type;
+/** True when a step's `run:` embeds a user-defined tool rather than a subworkflow. */
+export declare function isGalaxyUserToolRun(run: unknown): run is GalaxyUserToolStub;
 export declare const NormalizedFormat2WorkflowSchema: Schema.Struct<{
     class: Schema.Literal<["GalaxyWorkflow"]>;
     label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
@@ -56,6 +70,8 @@ export declare const NormalizedFormat2WorkflowSchema: Schema.Struct<{
         type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
         optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
         default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+        min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
+        max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
         format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
         collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
         position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -98,6 +114,8 @@ export declare const NormalizedFormat2StepSchema: Schema.Struct<{
             type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
             optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
             default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+            min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
+            max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
             format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
             collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
             position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -119,7 +137,10 @@ export declare const NormalizedFormat2StepSchema: Schema.Struct<{
             tool_id: typeof Schema.String;
             tool_version: Schema.NullOr<typeof Schema.String>;
         }>>;
-    }>, typeof Schema.String]>>>;
+    }>, Schema.TypeLiteral<{
+        class: Schema.Literal<["GalaxyUserTool"]>;
+        name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    }, readonly [Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>, typeof Schema.String]>>>;
     in: Schema.Array$<Schema.Struct<{
         id: typeof Schema.String;
         source: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;

package/dist/workflow/normalized/format2.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"format2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/format2.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAmBhC,eAAO,MAAM,gCAAgC;;;;;EAK3C,CAAC;AACH,MAAM,MAAM,0BAA0B,GAAG,OAAO,gCAAgC,CAAC,IAAI,CAAC;AAEtF,eAAO,MAAM,iCAAiC;;;;;;;;;EAW5C,CAAC;AACH,MAAM,MAAM,2BAA2B,GAAG,OAAO,iCAAiC,CAAC,IAAI,CAAC;AAExF,eAAO,MAAM,4BAA4B;;;;;;;;;;;;EAcvC,CAAC;AACH,MAAM,MAAM,sBAAsB,GAAG,OAAO,4BAA4B,CAAC,IAAI,CAAC;AAE9E,eAAO,MAAM,6BAA6B;;;;;;EAMxC,CAAC;AACH,MAAM,MAAM,uBAAuB,GAAG,OAAO,6BAA6B,CAAC,IAAI,CAAC;AAEhF;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;0EAMpC,CAAC;AACF,MAAM,MAAM,kBAAkB,GAAG,OAAO,wBAAwB,CAAC,IAAI,CAAC;AAEtE,sFAAsF;AACtF,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,OAAO,GAAG,GAAG,IAAI,kBAAkB,CAO3E;AAGD,eAAO,MAAM,+BAA+B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAe1C,CAAC;AACH,MAAM,MAAM,yBAAyB,GAAG,OAAO,+BAA+B,CAAC,IAAI,CAAC;AAEpF,eAAO,MAAM,2BAA2B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiCtC,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAI5E,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,OAAO,GAAG,yBAAyB,CAsBzE;AAyKD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,OAAO,GAAG,0BAA0B,EAAE,CA2B1E;AAED;;;;;;;;GAQG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,OAAO,GAAG,2BAA2B,EAAE,CAoB5E"}

package/dist/workflow/normalized/format2.js

@@ -42,6 +42,8 @@ export const NormalizedFormat2InputSchema = Schema.Struct({
     type: Schema.optional(Schema.NullOr(Schema.Union(Schema.String, Schema.Array(Schema.String)))),
     optional: Schema.optional(Schema.NullOr(Schema.Boolean)),
     default: Schema.optional(Schema.NullOr(Schema.Unknown)),
+    min: Schema.optional(Schema.NullOr(Schema.Number)),
+    max: Schema.optional(Schema.NullOr(Schema.Number)),
     format: Schema.optional(Schema.NullOr(Schema.Array(Schema.String))),
     collection_type: Schema.optional(Schema.NullOr(Schema.String)),
     position: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
@@ -53,6 +55,22 @@ export const NormalizedFormat2OutputSchema = Schema.Struct({
     outputSource: Schema.optional(Schema.NullOr(Schema.String)),
     type: Schema.optional(Schema.NullOr(Schema.String)),
 });
+/**
+ * An embedded user-defined tool under a step's `run:` (`class: GalaxyUserTool`).
+ * Only the discriminator is modelled; the rest of the tool definition passes
+ * through untouched. Mirrors gxformat2's `GalaxyUserToolStub`.
+ */
+export const GalaxyUserToolStubSchema = Schema.Struct({
+    class: Schema.Literal("GalaxyUserTool"),
+    name: Schema.optional(Schema.NullOr(Schema.String)),
+}, Schema.Record({ key: Schema.String, value: Schema.Unknown }));
+/** True when a step's `run:` embeds a user-defined tool rather than a subworkflow. */
+export function isGalaxyUserToolRun(run) {
+    return (run != null &&
+        typeof run === "object" &&
+        !Array.isArray(run) &&
+        run.class === "GalaxyUserTool");
+}
 // Workflow defined first; step uses suspend for forward ref
 export const NormalizedFormat2WorkflowSchema = Schema.Struct({
     class: Schema.Literal("GalaxyWorkflow"),
@@ -76,7 +94,7 @@ export const NormalizedFormat2StepSchema = Schema.Struct({
     tool_version: Schema.optional(Schema.NullOr(Schema.String)),
     tool_shed_repository: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
     type: Schema.optional(Schema.NullOr(Schema.String)),
-    run: Schema.optional(Schema.NullOr(Schema.Union(NormalizedFormat2WorkflowSchema, Schema.String))),
+    run: Schema.optional(Schema.NullOr(Schema.Union(NormalizedFormat2WorkflowSchema, GalaxyUserToolStubSchema, Schema.String))),
     in: Schema.Array(NormalizedFormat2StepInputSchema),
     out: Schema.Array(NormalizedFormat2StepOutputSchema),
     post_job_actions: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
@@ -115,7 +133,7 @@ export function normalizedFormat2(raw) {
 function _normalizeWorkflow(raw, subworkflows) {
     const inputs = _normalizeInputs(raw.inputs);
     const outputs = _normalizeOutputs(raw.outputs);
-    const steps = _normalizeSteps(raw.steps, subworkflows);
+    const steps = _normalizeSteps(raw.steps, subworkflows, inputs.length);
     const uniqueTools = _collectUniqueTools(steps);
     const result = {
         class: "GalaxyWorkflow",
@@ -189,13 +207,16 @@ function _normalizeOutputs(raw) {
     }
     return result;
 }
-function _normalizeSteps(raw, subworkflows) {
+function _normalizeSteps(raw, subworkflows, inputsOffset = 0) {
     if (!raw)
         return [];
     if (Array.isArray(raw)) {
+        // List-form steps without an explicit id get the index they will occupy in
+        // native form, where inputs come first -- so a numeric source like
+        // "1/out_file1" means the same thing before and after conversion.
         return raw.map((item, idx) => {
             const obj = item;
-            return _normalizeStep(obj, obj.id ?? String(idx), subworkflows);
+            return _normalizeStep(obj, obj.id ?? String(idx + inputsOffset), subworkflows);
         });
     }
     const result = [];
@@ -355,7 +376,7 @@ function _resolveRun(raw, subworkflows) {
             return dict["@import"];
         }
         // User-defined tool — pass through as-is
-        if (dict.class === "GalaxyUserTool") {
+        if (isGalaxyUserToolRun(dict)) {
             return dict;
         }
         // Inline workflow definition

package/dist/workflow/normalized/format2.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/index.d.ts

@@ -1,4 +1,4 @@
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, type GalaxyUserToolStub, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
 export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, } from "./native.js";
 export { toFormat2, type ToFormat2Options, type Format2StateOverride } from "./toFormat2.js";
 export { toNative, type ToNativeOptions } from "./toNative.js";
@@ -6,7 +6,7 @@ export { toFormat2Stateful, type StepConversionStatus, type StatefulExportResult
 export type { StepConversionFailureClass } from "./stateful-runner.js";
 export { toNativeStateful, type StatefulNativeResult } from "./toNativeStateful.js";
 export { ensureFormat2, ensureNative } from "./ensure.js";
-export { expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, } from "./expanded.js";
+export { expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, } from "./expanded.js";
 export { flattenCommentData, unflattenCommentData } from "./comments.js";
-export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
+export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/workflow/normalized/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,EACnB,KAAK,kBAAkB,EACvB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B,GACjC,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa,GACnB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAE,KAAK,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAE,KAAK,eAAe,EAAE,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB,GACxB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB,GACtB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}

package/dist/workflow/normalized/index.js

@@ -1,11 +1,11 @@
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, } from "./format2.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, } from "./format2.js";
 export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, } from "./native.js";
 export { toFormat2 } from "./toFormat2.js";
 export { toNative } from "./toNative.js";
 export { toFormat2Stateful, } from "./toFormat2Stateful.js";
 export { toNativeStateful } from "./toNativeStateful.js";
 export { ensureFormat2, ensureNative } from "./ensure.js";
-export { expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
+export { expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, } from "./expanded.js";
 export { flattenCommentData, unflattenCommentData } from "./comments.js";
-export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
+export { resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./labels.js";
 //# sourceMappingURL=index.js.map

package/dist/workflow/normalized/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,GAQpB,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,GAIpB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAoD,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAwB,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,GAIlB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,gBAAgB,EAA6B,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,gBAAgB,EAChB,mBAAmB,GAOpB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,aAAa,CAAC"}

package/dist/workflow/normalized/labels.d.ts

@@ -5,6 +5,13 @@
  */
 export declare const UNLABELED_INPUT_PREFIX = "_unlabeled_input_";
 export declare const UNLABELED_STEP_PREFIX = "_unlabeled_step_";
+/**
+ * Node id for a native step: its label, else a synthetic unlabeled sentinel.
+ *
+ * Shared by native→Format2 conversion and layout position matching so the two
+ * cannot drift.
+ */
+export declare function unlabeledNodeId(label: string | null | undefined, stepId: string | number, isInput: boolean): string;
 export declare function isUnlabeledInput(label: string): boolean;
 export declare function isUnlabeledStep(label: string): boolean;
 export declare function isUnlabeled(label: string): boolean;