@galaxy-tool-util/schema 1.6.0 → 1.7.0

package/dist/workflow/json-schemas.js

@@ -0,0 +1,39 @@
+/**
+ * Plain JSON Schema siblings of the Effect workflow schemas.
+ *
+ * Effect `Schema.Schema<A>` values are functions and do not survive
+ * `JSON.stringify`; downstream packagers that copy a schema verbatim into a
+ * runtime bundle need a plain-object JSON Schema instead. Mirrors the
+ * `parsedToolSchema` pattern in `schema/parsed-tool.ts`.
+ */
+import { JSONSchema } from "effect";
+import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
+/**
+ * Effect's `JSONSchema.make` emits inline `{$id: "/schemas/unknown", ...}`
+ * nodes wherever it encounters `Schema.Unknown` / `Schema.Any`. The draft
+ * schema hits this dozens of times (free-form `state`, `tool_state`,
+ * `default`, post-job actions, etc.), and Ajv refuses to compile a document
+ * with the same `$id` resolving to multiple distinct nodes. Stripping the
+ * `$id` leaves the node semantically equivalent (still accepts anything)
+ * and lets standard JSON Schema validators load the result.
+ */
+function stripDuplicateUnknownIds(node) {
+    if (node === null || typeof node !== "object")
+        return;
+    if (Array.isArray(node)) {
+        for (const item of node)
+            stripDuplicateUnknownIds(item);
+        return;
+    }
+    const obj = node;
+    if (obj.$id === "/schemas/unknown")
+        delete obj.$id;
+    for (const k of Object.keys(obj))
+        stripDuplicateUnknownIds(obj[k]);
+}
+const draftJsonSchema = JSONSchema.make(GalaxyWorkflowDraftSchema, {
+    target: "jsonSchema2020-12",
+});
+stripDuplicateUnknownIds(draftJsonSchema);
+export const galaxyWorkflowDraftJsonSchema = draftJsonSchema;
+//# sourceMappingURL=json-schemas.js.map

package/dist/workflow/json-schemas.js.map

@@ -0,0 +1 @@
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package/dist/workflow/normalized/toFormat2.js

@@ -159,13 +159,18 @@ function _buildToolFormat2Step(step, labelMap, options) {
     }
     const inList = _buildFormat2StepInputs(step, labelMap);
     const outList = _buildFormat2StepOutputs(step);
-    // Stateful override: if the caller provides a per-step state encoder
-    // and it returns a non-null result, use its state (and optional `in`
-    // block entries) instead of the default schema-free passthrough.
+    // Tool state routing mirrors gxformat2's state_encode_to_format2 contract:
+    // when the per-step encoder succeeds, its schema-aware result is the clean
+    // `state` block (connections/runtime lifted into `in:`); when it returns null
+    // (no encoder, precheck/validation/conversion failure), we fall back to the
+    // raw native `tool_state` passthrough. Only one of the two fields is ever set,
+    // so a step carrying `tool_state` and no `state` unambiguously signals
+    // unconverted/state-unaware output (validators skip it).
     const override = options?.stateEncodeToFormat2?.(step);
+    let state;
     let toolState = null;
     if (override != null) {
-        toolState = Object.keys(override.state).length > 0 ? override.state : null;
+        state = override.state;
         if (override.in) {
             _mergeInOverrides(inList, override.in);
         }
@@ -189,6 +194,7 @@ function _buildToolFormat2Step(step, labelMap, options) {
         tool_shed_repository: step.tool_shed_repository,
         in: inList,
         out: outList,
+        state,
         tool_state: toolState,
         position: step.position,
         when: step.when ?? undefined,

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

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

@@ -1 +1 @@
-{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAuGH;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA4BjE"}
+{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAsIH;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA6BjE"}

package/dist/workflow/semantic-validators.js

@@ -98,6 +98,37 @@ function validateInputParameter(inputParam) {
         }
     }
 }
+/**
+ * True when a step's `state`/`tool_state` field actually carries content.
+ *
+ * Non-empty semantics: null/undefined, an empty object, and a blank or `{}`
+ * JSON string all count as unspecified — so an empty `state: {}` left by
+ * conversion does not falsely conflict with a populated `tool_state`. Mirrors
+ * gxformat2 `_semantic_validators._state_is_specified`.
+ */
+function _stateIsSpecified(value) {
+    if (value == null)
+        return false;
+    if (typeof value === "string") {
+        const s = value.trim();
+        return s !== "" && s !== "{}";
+    }
+    if (typeof value === "object")
+        return Object.keys(value).length > 0;
+    return Boolean(value);
+}
+/**
+ * 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.
+ */
+function validateStep(step) {
+    if (_stateIsSpecified(step.state) && _stateIsSpecified(step.tool_state)) {
+        throw new Error("Workflow step specifies both 'state' and 'tool_state'; only one may be set");
+    }
+}
 /**
  * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
  * Recurses into inline subworkflows under step.run.
@@ -126,6 +157,7 @@ export function validateWorkflowSemantics(workflow) {
     for (const step of iterSteps) {
         if (!step || typeof step !== "object")
             continue;
+        validateStep(step);
         const run = step.run;
         if (run &&
             typeof run === "object" &&

package/dist/workflow/semantic-validators.js.map

@@ -1 +1 @@
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package/dist/workflow/state-merge.d.ts

@@ -9,8 +9,29 @@
  * for backward compatibility.
  */
 import type { ToolParameterModel } from "../schema/bundle-types.js";
+import type { NormalizedFormat2StepInput } from "./normalized/format2.js";
 import { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen } from "./walk-helpers.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen };
+/**
+ * Build the connections map for a format2 step's `in` block so a verbatim
+ * native `tool_state` block can be validated through the native path.
+ *
+ * injectConnectionsIntoState consumes only the *keys* of this map — it matches
+ * them against state paths and substitutes ConnectedValue markers — so the value
+ * is a bare presence marker. The connection's source is intentionally irrelevant
+ * here; encoding it would be dead computation.
+ */
+export declare function nativeConnectionsFromFormat2In(inputs: readonly NormalizedFormat2StepInput[]): Record<string, true>;
+export interface InjectConnectionsOptions {
+    /**
+     * Target the `workflow_step_linked` representation. A connected `multiple`
+     * select is encoded there as a single-element list `[{ConnectedValue}]` (the
+     * select-multiple linked schema accepts ConnectedValue only as an array item,
+     * per Galaxy's parameter_specification.yml), whereas every other parameter —
+     * and the native representation — uses a bare `{ConnectedValue}`.
+     */
+    linked?: boolean;
+}
 /**
  * Inject ConnectedValue markers into a state dict for all connections.
  *
@@ -20,7 +41,7 @@ export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen }
  *
  * @returns remaining unmatched connection paths (empty if all consumed)
  */
-export declare function injectConnectionsIntoState(toolInputs: ToolParameterModel[], state: Record<string, unknown>, connections: Record<string, unknown>): Record<string, unknown>;
+export declare function injectConnectionsIntoState(toolInputs: ToolParameterModel[], state: Record<string, unknown>, connections: Record<string, unknown>, options?: InjectConnectionsOptions): Record<string, unknown>;
 /**
  * Strip ConnectedValue markers from a state dict using the parameter tree.
  *

package/dist/workflow/state-merge.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"state-merge.d.ts","sourceRoot":"","sources":["../../src/workflow/state-merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAGpE,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,EAChB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,eAAe,EAAE,CAAC;AAIjF;;;;;;;;GAQG;AACH,wBAAgB,0BAA0B,CACxC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACnC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAkBzB;AAID;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,IAAI,CAWN"}
+{"version":3,"file":"state-merge.d.ts","sourceRoot":"","sources":["../../src/workflow/state-merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AACpE,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,yBAAyB,CAAC;AAG1E,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,EAChB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,eAAe,EAAE,CAAC;AAIjF;;;;;;;;GAQG;AACH,wBAAgB,8BAA8B,CAC5C,MAAM,EAAE,SAAS,0BAA0B,EAAE,GAC5C,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,CAQtB;AAID,MAAM,WAAW,wBAAwB;IACvC;;;;;;OAMG;IACH,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAOD;;;;;;;;GAQG;AACH,wBAAgB,0BAA0B,CACxC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACpC,OAAO,CAAC,EAAE,wBAAwB,GACjC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAoBzB;AAID;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,IAAI,CAWN"}

package/dist/workflow/state-merge.js

@@ -13,7 +13,29 @@ import { walkNativeState, SKIP_VALUE } from "./walker.js";
 import { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 // Re-export helpers so existing importers don't break
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen };
-// --- Main injection function ---
+// --- Connection-key construction ---
+/**
+ * Build the connections map for a format2 step's `in` block so a verbatim
+ * native `tool_state` block can be validated through the native path.
+ *
+ * injectConnectionsIntoState consumes only the *keys* of this map — it matches
+ * them against state paths and substitutes ConnectedValue markers — so the value
+ * is a bare presence marker. The connection's source is intentionally irrelevant
+ * here; encoding it would be dead computation.
+ */
+export function nativeConnectionsFromFormat2In(inputs) {
+    const connections = {};
+    for (const input of inputs) {
+        if (input.id && input.source) {
+            connections[input.id] = true;
+        }
+    }
+    return connections;
+}
+function isMultipleSelect(input) {
+    const p = input;
+    return p.parameter_type === "gx_select" && p.multiple === true;
+}
 /**
  * Inject ConnectedValue markers into a state dict for all connections.
  *
@@ -23,12 +45,14 @@ export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen }
  *
  * @returns remaining unmatched connection paths (empty if all consumed)
  */
-export function injectConnectionsIntoState(toolInputs, state, connections) {
+export function injectConnectionsIntoState(toolInputs, state, connections, options) {
     const remaining = { ...connections };
-    const result = walkNativeState(connections, toolInputs, state, (_input, value, statePath) => {
+    const result = walkNativeState(connections, toolInputs, state, (input, value, statePath) => {
         if (statePath in remaining) {
             delete remaining[statePath];
-            return { ...CONNECTED_VALUE };
+            return options?.linked && isMultipleSelect(input)
+                ? [{ ...CONNECTED_VALUE }]
+                : { ...CONNECTED_VALUE };
         }
         return value === undefined ? SKIP_VALUE : value;
     }, { preserveUnknownKeys: true });

package/dist/workflow/state-merge.js.map

@@ -1 +1 @@
-{"version":3,"file":"state-merge.js","sourceRoot":"","sources":["../../src/workflow/state-merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AACzE,OAAO,EAAE,eAAe,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,mBAAmB,CAAC;AAE3B,sDAAsD;AACtD,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,eAAe,EAAE,CAAC;AAEjF,kCAAkC;AAElC;;;;;;;;GAQG;AACH,MAAM,UAAU,0BAA0B,CACxC,UAAgC,EAChC,KAA8B,EAC9B,WAAoC;IAEpC,MAAM,SAAS,GAAG,EAAE,GAAG,WAAW,EAAE,CAAC;IACrC,MAAM,MAAM,GAAG,eAAe,CAC5B,WAAW,EACX,UAAU,EACV,KAAK,EACL,CAAC,MAAM,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE;QAC3B,IAAI,SAAS,IAAI,SAAS,EAAE,CAAC;YAC3B,OAAO,SAAS,CAAC,SAAS,CAAC,CAAC;YAC5B,OAAO,EAAE,GAAG,eAAe,EAAE,CAAC;QAChC,CAAC;QACD,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC;IAClD,CAAC,EACD,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAC9B,CAAC;IACF,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACxD,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,mCAAmC;AAEnC;;;;;;GAMG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAgC,EAChC,KAA8B;IAE9B,MAAM,OAAO,GAAG,eAAe,CAC7B,EAAE,EACF,UAAU,EACV,KAAK,EACL,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAChB,gBAAgB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EACjF,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAC9B,CAAC;IACF,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACxD,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;AAChC,CAAC"}
+{"version":3,"file":"state-merge.js","sourceRoot":"","sources":["../../src/workflow/state-merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AACzE,OAAO,EAAE,eAAe,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,mBAAmB,CAAC;AAE3B,sDAAsD;AACtD,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,eAAe,EAAE,CAAC;AAEjF,sCAAsC;AAEtC;;;;;;;;GAQG;AACH,MAAM,UAAU,8BAA8B,CAC5C,MAA6C;IAE7C,MAAM,WAAW,GAAyB,EAAE,CAAC;IAC7C,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,KAAK,CAAC,EAAE,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;YAC7B,WAAW,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC;QAC/B,CAAC;IACH,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC;AAeD,SAAS,gBAAgB,CAAC,KAAyB;IACjD,MAAM,CAAC,GAAG,KAAwD,CAAC;IACnE,OAAO,CAAC,CAAC,cAAc,KAAK,WAAW,IAAI,CAAC,CAAC,QAAQ,KAAK,IAAI,CAAC;AACjE,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,0BAA0B,CACxC,UAAgC,EAChC,KAA8B,EAC9B,WAAoC,EACpC,OAAkC;IAElC,MAAM,SAAS,GAAG,EAAE,GAAG,WAAW,EAAE,CAAC;IACrC,MAAM,MAAM,GAAG,eAAe,CAC5B,WAAW,EACX,UAAU,EACV,KAAK,EACL,CAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE;QAC1B,IAAI,SAAS,IAAI,SAAS,EAAE,CAAC;YAC3B,OAAO,SAAS,CAAC,SAAS,CAAC,CAAC;YAC5B,OAAO,OAAO,EAAE,MAAM,IAAI,gBAAgB,CAAC,KAAK,CAAC;gBAC/C,CAAC,CAAC,CAAC,EAAE,GAAG,eAAe,EAAE,CAAC;gBAC1B,CAAC,CAAC,EAAE,GAAG,eAAe,EAAE,CAAC;QAC7B,CAAC;QACD,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC;IAClD,CAAC,EACD,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAC9B,CAAC;IACF,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACxD,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,mCAAmC;AAEnC;;;;;;GAMG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAgC,EAChC,KAA8B;IAE9B,MAAM,OAAO,GAAG,eAAe,CAC7B,EAAE,EACF,UAAU,EACV,KAAK,EACL,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAChB,gBAAgB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EACjF,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAC9B,CAAC;IACF,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACxD,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;AAChC,CAAC"}

package/dist/workflow/stateful-convert.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"stateful-convert.d.ts","sourceRoot":"","sources":["../../src/workflow/stateful-convert.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EACV,kBAAkB,EAGnB,MAAM,2BAA2B,CAAC;AACnC,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAQnE;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,SAAS,EAAE,kBAAkB,EAAE,KAAK,EAAE,OAAO,GAAG,OAAO,CA8BzF;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,SAAS,EAAE,kBAAkB,EAAE,KAAK,EAAE,OAAO,GAAG,OAAO,CAqBzF;AAID,MAAM,WAAW,qBAAqB;IACpC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC5B;AAUD;;;;;;;;;GASG;AACH,wBAAgB,qBAAqB,CACnC,UAAU,EAAE,oBAAoB,EAChC,UAAU,EAAE,kBAAkB,EAAE,GAC/B,qBAAqB,CAqEvB;AAID;;;;;GAKG;AACH,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAMzB"}

package/dist/workflow/stateful-convert.js

@@ -69,6 +69,10 @@ export function reverseScalarValue(toolInput, value) {
 }
 /** Data parameter types — always go to `in` block, never to state. */
 const DATA_PARAM_TYPES = new Set(["gx_data", "gx_data_collection"]);
+/** Read `optional` defensively — CWL parameter models lack the field. */
+function isOptionalParam(toolInput) {
+    return toolInput.optional === true;
+}
 /**
  * Convert a native step's tool_state to format2 state + in block.
  *
@@ -87,13 +91,18 @@ export function convertStateToFormat2(nativeStep, toolInputs) {
     const inBlock = {};
     const leafCallback = (toolInput, value, statePath) => {
         const paramType = toolInput.parameter_type;
-        // Data parameters: always to `in` block
+        // Data parameters: never to state. Connection wins over any marker.
         if (DATA_PARAM_TYPES.has(paramType)) {
-            if (isConnectedValue(value) || connectedPaths.has(statePath)) {
+            if (connectedPaths.has(statePath) || isConnectedValue(value)) {
                 // Connected data param — recorded via input_connections, handled by structural conversion
+                return SKIP_VALUE;
             }
             if (isRuntimeValue(value)) {
-                inBlock[statePath] = "runtime_value";
+                // Disconnected runtime: keep placeholder only when required; omit when optional.
+                if (!isOptionalParam(toolInput)) {
+                    inBlock[statePath] = "runtime_value";
+                }
+                return SKIP_VALUE;
             }
             return SKIP_VALUE;
         }
@@ -115,14 +124,15 @@ export function convertStateToFormat2(nativeStep, toolInputs) {
             }
             return value;
         }
-        // ConnectedValue → record in `in` block, skip from state
-        if (isConnectedValue(value)) {
-            // Connection source handled by structural conversion's input_connections
+        // Connection wins over any marker — source handled by structural conversion.
+        if (connectedPaths.has(statePath) || isConnectedValue(value)) {
             return SKIP_VALUE;
         }
-        // RuntimeValue → record in `in` block, skip from state
+        // Disconnected runtime: keep placeholder only when required; omit when optional.
         if (isRuntimeValue(value)) {
-            inBlock[statePath] = "runtime_value";
+            if (!isOptionalParam(toolInput)) {
+                inBlock[statePath] = "runtime_value";
+            }
             return SKIP_VALUE;
         }
         // Null / "null" values → skip

package/dist/workflow/stateful-convert.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.6.0",
+  "version": "1.7.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {