@galaxy-tool-util/schema 1.12.0 → 1.14.0

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

@@ -1 +1 @@
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+{"version":3,"file":"labels.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,eAAO,MAAM,sBAAsB,sBAAsB,CAAC;AAC1D,eAAO,MAAM,qBAAqB,qBAAqB,CAAC;AAExD;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,EAChC,MAAM,EAAE,MAAM,GAAG,MAAM,EACvB,OAAO,EAAE,OAAO,GACf,MAAM,CAGR;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEvD;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEtD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAElD;AAED,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,OAAO,CAEhF;AAED;;GAEG;AACH,qBAAa,MAAM;IACjB,OAAO,CAAC,UAAU,CAAqB;IACvC,OAAO,CAAC,eAAe,CAAK;IAE5B,oBAAoB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,MAAM;CAQ/D;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,EAAE,EAAE,MAAM,CAAA;CAAE,GAAG,MAAM,CAEtF;AAED;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAU5E;AAED;;;;;GAKG;AACH,wBAAgB,sBAAsB,CACpC,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC,MAAM,CAAC,GAC7C,CAAC,MAAM,EAAE,MAAM,CAAC,CAkBlB"}

package/dist/workflow/normalized/labels.js

@@ -5,6 +5,17 @@
  */
 export const UNLABELED_INPUT_PREFIX = "_unlabeled_input_";
 export 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 function unlabeledNodeId(label, stepId, isInput) {
+    if (label != null)
+        return label;
+    return `${isInput ? UNLABELED_INPUT_PREFIX : UNLABELED_STEP_PREFIX}${stepId}`;
+}
 export function isUnlabeledInput(label) {
     return label.startsWith(UNLABELED_INPUT_PREFIX);
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"labels.js","sourceRoot":"","sources":["../../../src/workflow/normalized/labels.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,MAAM,CAAC,MAAM,sBAAsB,GAAG,mBAAmB,CAAC;AAC1D,MAAM,CAAC,MAAM,qBAAqB,GAAG,kBAAkB,CAAC;AAExD;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAgC,EAChC,MAAuB,EACvB,OAAgB;IAEhB,IAAI,KAAK,IAAI,IAAI;QAAE,OAAO,KAAK,CAAC;IAChC,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,qBAAqB,GAAG,MAAM,EAAE,CAAC;AAChF,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,KAAa;IAC5C,OAAO,KAAK,CAAC,UAAU,CAAC,sBAAsB,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAa;IAC3C,OAAO,KAAK,CAAC,UAAU,CAAC,qBAAqB,CAAC,CAAC;AACjD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAa;IACvC,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,eAAe,CAAC,KAAK,CAAC,CAAC;AAC3D,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,KAAgC;IACrE,OAAO,CAAC,KAAK,IAAI,KAAK,CAAC,UAAU,CAAC,oBAAoB,CAAC,CAAC;AAC1D,CAAC;AAED;;GAEG;AACH,MAAM,OAAO,MAAM;IACT,UAAU,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,eAAe,GAAG,CAAC,CAAC;IAE5B,oBAAoB,CAAC,KAAgC;QACnD,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;YAClB,IAAI,CAAC,eAAe,IAAI,CAAC,CAAC;YAC1B,KAAK,GAAG,qBAAqB,IAAI,CAAC,eAAe,EAAE,CAAC;QACtD,CAAC;QACD,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAC3B,OAAO,KAAK,CAAC;IACf,CAAC;CACF;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAA2C;IAC5E,OAAO,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,EAAE,CAAC;AAC/B,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,qBAAqB,CAAC,IAAa,EAAE,OAAe;IAClE,IACE,OAAO,IAAI,KAAK,QAAQ;QACxB,IAAI,KAAK,IAAI;QACb,OAAQ,IAAgC,CAAC,KAAK,KAAK,QAAQ;QACzD,IAAgC,CAAC,KAAgB,CAAC,MAAM,GAAG,CAAC,EAC9D,CAAC;QACD,OAAQ,IAAgC,CAAC,KAAe,CAAC;IAC3D,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CACpC,KAAa,EACb,WAA8C;IAE9C,MAAM,SAAS,GAAG,WAAW,YAAY,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC;IAC1F,yDAAyD;IACzD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC;IAE9C,KAAK,MAAM,KAAK,IAAI,SAAS,EAAE,CAAC;QAC9B,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;YACpB,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;QAC3B,CAAC;QACD,IAAI,KAAK,CAAC,UAAU,CAAC,KAAK,GAAG,GAAG,CAAC,EAAE,CAAC;YAClC,OAAO,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;QAChD,CAAC;IACH,CAAC;IACD,IAAI,KAAK,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,GAAG,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;AAC3B,CAAC"}

package/dist/workflow/normalized/toFormat2.d.ts

@@ -5,6 +5,7 @@
  */
 import type { NormalizedNativeStep } from "./native.js";
 import type { NormalizedFormat2Workflow } from "./format2.js";
+export declare const INPUT_STEP_TYPES: Set<string>;
 /**
  * Per-step callback result: a replacement format2 state dict + optional `in`
  * block overrides (flat path → source). Return null to fall back to the

package/dist/workflow/normalized/toFormat2.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAUtB;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F"}
+{"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAStB,eAAO,MAAM,gBAAgB,aAAsE,CAAC;AAEpG;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F"}

package/dist/workflow/normalized/toFormat2.js

@@ -4,12 +4,13 @@
  * Port of gxformat2/normalized/_conversion.py to_format2 + helpers.
  */
 import { normalizedNative } from "./native.js";
+import { isGalaxyUserToolRun } from "./format2.js";
 import { flattenCommentData } from "./comments.js";
-import { UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, isUnlabeled, Labels } from "./labels.js";
+import { isUnlabeled, Labels, unlabeledNodeId } from "./labels.js";
 // Effect schemas produce deeply-readonly types. We build plain objects
 // and cast — runtime semantics are identical.
 // Step types that represent workflow inputs
-const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
+export const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
 /**
  * Convert a native Galaxy workflow to normalized Format2.
  */
@@ -21,15 +22,7 @@ function _buildFormat2Workflow(wf, options) {
     // Build label map: step key → label string
     const labelMap = new Map();
     for (const [key, step] of Object.entries(wf.steps)) {
-        if (step.label != null) {
-            labelMap.set(String(key), step.label);
-        }
-        else if (INPUT_STEP_TYPES.has(step.type)) {
-            labelMap.set(String(key), `${UNLABELED_INPUT_PREFIX}${step.id}`);
-        }
-        else {
-            labelMap.set(String(key), `${UNLABELED_STEP_PREFIX}${step.id}`);
-        }
+        labelMap.set(String(key), unlabeledNodeId(step.label, step.id, INPUT_STEP_TYPES.has(step.type)));
     }
     // Build workflow outputs from step workflow_outputs
     const labels = new Labels();
@@ -98,7 +91,7 @@ function _nativeInputToFormat2Type(stepType, toolState) {
     return "data";
 }
 function _buildInputParam(step) {
-    const stepId = step.label ?? `${UNLABELED_INPUT_PREFIX}${step.id}`;
+    const stepId = unlabeledNodeId(step.label, step.id, true);
     const inputType = _nativeInputToFormat2Type(step.type, step.tool_state);
     const result = { id: stepId, type: inputType };
     const ts = step.tool_state;
@@ -123,6 +116,23 @@ function _buildInputParam(step) {
             }
         }
     }
+    if (inputType === "int" || inputType === "float") {
+        const validators = ts.validators;
+        if (Array.isArray(validators)) {
+            for (const validator of validators) {
+                if (validator &&
+                    typeof validator === "object" &&
+                    validator.type === "in_range" &&
+                    !validator.negate) {
+                    if (typeof validator.min === "number")
+                        result.min = validator.min;
+                    if (typeof validator.max === "number")
+                        result.max = validator.max;
+                    break;
+                }
+            }
+        }
+    }
     if (step.annotation)
         result.doc = step.annotation;
     if (step.position)
@@ -152,9 +162,7 @@ function _buildFormat2Step(step, labelMap, options) {
     return _buildToolFormat2Step(step, labelMap, options);
 }
 function _buildToolFormat2Step(step, labelMap, options) {
-    // User-defined tool: tool_representation with class GalaxyUserTool
-    const toolRep = step.tool_representation;
-    if (toolRep && toolRep.class === "GalaxyUserTool") {
+    if (isGalaxyUserToolRun(step.tool_representation)) {
         return _buildUserToolFormat2Step(step, labelMap);
     }
     const inList = _buildFormat2StepInputs(step, labelMap);
@@ -176,13 +184,7 @@ function _buildToolFormat2Step(step, labelMap, options) {
         }
     }
     else {
-        // Default: copy tool_state, strip bookkeeping keys
-        const ts = { ...step.tool_state };
-        delete ts.__page__;
-        delete ts.__rerun_remap_job_id__;
-        if (Object.keys(ts).length > 0) {
-            toolState = ts;
-        }
+        toolState = _passthroughToolState(step);
     }
     const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
     return {
@@ -202,6 +204,15 @@ function _buildToolFormat2Step(step, labelMap, options) {
         errors: step.errors ?? undefined,
     };
 }
+/** Default: copy tool_state verbatim, minus bookkeeping keys; null when nothing is left. */
+function _passthroughToolState(step) {
+    const ts = { ...step.tool_state };
+    delete ts.__page__;
+    delete ts.__rerun_remap_job_id__;
+    return Object.keys(ts).length > 0 ? ts : null;
+}
+// The stateful encoder resolves tools by tool_id, which a user-defined tool
+// step doesn't have, so its tool_state always passes through verbatim.
 function _buildUserToolFormat2Step(step, labelMap) {
     const inList = _buildFormat2StepInputs(step, labelMap);
     const outList = _buildFormat2StepOutputs(step);
@@ -213,7 +224,11 @@ function _buildUserToolFormat2Step(step, labelMap) {
         run: step.tool_representation,
         in: inList,
         out: outList,
+        tool_state: _passthroughToolState(step),
         position: step.position,
+        when: step.when ?? undefined,
+        uuid: step.uuid ?? undefined,
+        errors: step.errors ?? undefined,
     };
 }
 function _buildSubworkflowFormat2Step(step, labelMap, options) {
@@ -393,7 +408,7 @@ function _replaceAnonymousOutputReferences(outputParams, fmt2Steps) {
     const runsByLabel = new Map();
     for (const step of fmt2Steps) {
         const label = step.label ?? step.id;
-        if (step.run && typeof step.run === "object") {
+        if (step.run && typeof step.run === "object" && !isGalaxyUserToolRun(step.run)) {
             runsByLabel.set(String(label), step.run);
         }
     }

package/dist/workflow/normalized/toFormat2.js.map

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

@@ -4,7 +4,7 @@
  * Port of gxformat2/normalized/_conversion.py to_native + helpers.
  */
 import type { NormalizedNativeWorkflow } from "./native.js";
-import type { NormalizedFormat2Step } from "./format2.js";
+import type { NormalizedFormat2Step, NormalizedFormat2Input } from "./format2.js";
 export interface ToNativeOptions {
     /**
      * Per-step callback: given a format2 step and its merged pre-native
@@ -17,4 +17,19 @@ export interface ToNativeOptions {
  * Convert a Format2 workflow to normalized native Galaxy format.
  */
 export declare function toNative(raw: unknown, options?: ToNativeOptions): NormalizedNativeWorkflow;
+/**
+ * Native step label for a Format2 input at `orderIndex`.
+ *
+ * Inputs are labeled by `id`, falling back to `Input <orderIndex>`.
+ * Sentinel labels (`_unlabeled_*`) are cleared to null.
+ */
+export declare function nativeInputLabel(inp: NormalizedFormat2Input, orderIndex: number): string | null;
+/**
+ * Native step label for a Format2 step.
+ *
+ * An explicit `label` wins; otherwise a non-numeric `id` is a user label and
+ * numeric ids are auto-assigned indices. Sentinel labels (`_unlabeled_*`) are
+ * cleared to null.
+ */
+export declare function nativeStepLabel(step: NormalizedFormat2Step): string | null | undefined;
 //# sourceMappingURL=toNative.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"toNative.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toNative.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAwB,MAAM,aAAa,CAAC;AAClF,OAAO,KAAK,EAEV,qBAAqB,EACrB,sBAAsB,EAEvB,MAAM,cAAc,CAAC;AA2FtB,MAAM,WAAW,eAAe;IAC9B;;;;OAIG;IACH,mBAAmB,CAAC,EAAE,CACpB,IAAI,EAAE,qBAAqB,EAC3B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CACrC;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,wBAAwB,CAS1F;AA4kBD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,sBAAsB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG/F;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,qBAAqB,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAUtF"}

package/dist/workflow/normalized/toNative.js

@@ -3,7 +3,7 @@
  *
  * Port of gxformat2/normalized/_conversion.py to_native + helpers.
  */
-import { normalizedFormat2 } from "./format2.js";
+import { isGalaxyUserToolRun, normalizedFormat2 } from "./format2.js";
 import { unflattenCommentData } from "./comments.js";
 import { isUnlabeled, resolveSourceReference } from "./labels.js";
 function _uuid() {
@@ -81,23 +81,14 @@ const POST_JOB_ACTIONS = {
  * Convert a Format2 workflow to normalized native Galaxy format.
  */
 export function toNative(raw, options) {
-    let wf;
-    if (_isNormalizedFormat2(raw)) {
-        wf = raw;
-    }
-    else {
-        wf = normalizedFormat2(raw);
-    }
+    // Normalize unconditionally: `normalizedFormat2` is idempotent, and no
+    // top-level shape check can tell an already-normalized workflow from a raw
+    // one with list-form `inputs`/`steps` but dict-form `in`/`out` on its steps.
+    const wf = normalizedFormat2(raw);
     const ctx = new ConversionContext(options);
     _registerLabels(wf, ctx);
     return _buildNativeWorkflow(wf, ctx);
 }
-function _isNormalizedFormat2(raw) {
-    if (raw == null || typeof raw !== "object")
-        return false;
-    const obj = raw;
-    return obj.class === "GalaxyWorkflow" && Array.isArray(obj.inputs) && Array.isArray(obj.steps);
-}
 function _registerLabels(wf, ctx) {
     for (let i = 0; i < wf.inputs.length; i++) {
         const inp = wf.inputs[i];
@@ -157,7 +148,7 @@ function _buildNativeWorkflow(wf, ctx) {
 // --- Input step building ---
 function _buildInputStep(inp, orderIndex) {
     const rawLabel = inp.id || `Input ${orderIndex}`;
-    const label = isUnlabeled(rawLabel) ? undefined : rawLabel;
+    const label = nativeInputLabel(inp, orderIndex);
     let inputType = inp.type;
     let multiple = false;
     if (Array.isArray(inputType)) {
@@ -201,6 +192,13 @@ function _buildInputStep(inp, orderIndex) {
         toolState.collection_type = inp.collection_type;
     if (inp.default != null)
         toolState.default = inp.default;
+    if (stepType === "parameter_input" &&
+        ["integer", "int", "float"].includes(typeStr) &&
+        (inp.min != null || inp.max != null)) {
+        toolState.validators = [
+            { type: "in_range", min: inp.min ?? null, max: inp.max ?? null, negate: false },
+        ];
+    }
     // Copy extra fields
     for (const key of [
         "restrictions",
@@ -255,10 +253,7 @@ function _buildStep(step, orderIndex, ctx) {
 function _resolveStepType(step) {
     if (step.run != null) {
         if (typeof step.run === "object") {
-            const runObj = step.run;
-            if (runObj.class === "GalaxyUserTool")
-                return "tool";
-            return "subworkflow";
+            return isGalaxyUserToolRun(step.run) ? "tool" : "subworkflow";
         }
         if (typeof step.run === "string")
             return "subworkflow";
@@ -267,14 +262,9 @@ function _resolveStepType(step) {
     return STEP_TYPE_ALIASES[rawType] ?? rawType;
 }
 function _buildToolStep(step, orderIndex, ctx) {
-    // Detect GalaxyUserTool in run field
-    let toolRepresentation;
-    if (step.run && typeof step.run === "object") {
-        const runObj = step.run;
-        if (runObj.class === "GalaxyUserTool") {
-            toolRepresentation = runObj;
-        }
-    }
+    const toolRepresentation = isGalaxyUserToolRun(step.run)
+        ? step.run
+        : undefined;
     const toolState = { __page__: 0 };
     const connect = _extractConnections(step);
     const runtimeInputs = step.runtime_inputs ?? [];
@@ -309,7 +299,7 @@ function _buildToolStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "tool",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name: toolId ?? toolRepresentation?.name ?? "User Defined Tool",
         annotation: step.doc ?? "",
         tool_id: toolId,
@@ -355,7 +345,7 @@ function _buildSubworkflowStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "subworkflow",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         annotation: step.doc ?? "",
         tool_state: {},
         subworkflow,
@@ -380,7 +370,7 @@ function _buildPauseStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "pause",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name,
         annotation: step.doc ?? "",
         tool_state: { name },
@@ -409,7 +399,7 @@ function _buildPickValueStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "pick_value",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name,
         annotation: step.doc ?? "",
         tool_state: toolState,
@@ -591,7 +581,24 @@ function _buildNativeComments(wf, ctx) {
     return result;
 }
 // --- Helpers ---
-function _stepLabel(step) {
+/**
+ * Native step label for a Format2 input at `orderIndex`.
+ *
+ * Inputs are labeled by `id`, falling back to `Input <orderIndex>`.
+ * Sentinel labels (`_unlabeled_*`) are cleared to null.
+ */
+export function nativeInputLabel(inp, orderIndex) {
+    const rawLabel = inp.id || `Input ${orderIndex}`;
+    return isUnlabeled(rawLabel) ? null : rawLabel;
+}
+/**
+ * Native step label for a Format2 step.
+ *
+ * An explicit `label` wins; otherwise a non-numeric `id` is a user label and
+ * numeric ids are auto-assigned indices. Sentinel labels (`_unlabeled_*`) are
+ * cleared to null.
+ */
+export function nativeStepLabel(step) {
     if (step.label != null) {
         if (isUnlabeled(step.label))
             return null;

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

@@ -1 +1 @@
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package/dist/workflow/semantic-validators.d.ts

@@ -10,6 +10,15 @@
  * (runtime tool-state validation): these are structural-but-cross-field
  * Format2 rules.
  */
+export declare function validateInputParameter(inputParam: unknown): void;
+/**
+ * Validate cross-field rules on a single workflow step.
+ *
+ * Enforces that `state` and `tool_state` are mutually exclusive (the schema doc
+ * says "Only one or the other should be specified") — they are two encodings of
+ * the same tool state, so carrying both is ambiguous.
+ */
+export declare function validateStep(step: Record<string, unknown>): void;
 /**
  * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
  * Recurses into inline subworkflows under step.run.

package/dist/workflow/semantic-validators.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AA0DH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,OAAO,GAAG,IAAI,CA2DhE;AAoBD;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAIhE;AAED;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA+BjE"}