@galaxy-tool-util/schema 0.1.0 → 0.4.0

package/dist/workflow/lint-rules.js

@@ -0,0 +1,15 @@
+/**
+ * Lint rule classes.
+ *
+ * Each `Linter` subclass carries metadata only (severity, applies_to,
+ * profile). Emission happens in `lint.ts` via `LintContext.warn`/`error`
+ * with `linter=<Subclass>`.
+ */
+import { Linter } from "./linting.js";
+/** Native workflow step keys must be string representations of integers. */
+export class NativeStepKeyNotInteger extends Linter {
+    static severity = "error";
+    static applies_to = ["native"];
+    static profile = "structural";
+}
+//# sourceMappingURL=lint-rules.js.map

package/dist/workflow/lint-rules.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"lint-rules.js","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,MAAM,OAAO,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,QAAQ,CAAU,CAAC;IACxC,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC"}

package/dist/workflow/lint.d.ts

@@ -1,25 +1,11 @@
 /**
  * Workflow linting — structural checks and best-practice warnings.
  *
- * Port of gxformat2's lint.py + linting.py. Checks workflow structure,
- * output labels, step errors, tool references, output source resolution,
- * input default types, and report markdown.
+ * Port of gxformat2's lint.py. Emission primitives live in `linting.ts`
+ * (LintContext / LintMessage / Linter base); rule classes in `lint-rules.ts`.
  */
-export declare class LintContext {
-    errors: string[];
-    warnings: string[];
-    private _prefix;
-    constructor(prefix?: string);
-    error(message: string): void;
-    warn(message: string): void;
-    child(prefix: string): LintContext;
-}
-export interface LintResult {
-    errors: string[];
-    warnings: string[];
-    error_count: number;
-    warn_count: number;
-}
+import { type LintResult } from "./linting.js";
+export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, type LintLevel, type LintResult, type LinterRef, type EmitOptions, } from "./linting.js";
 /**
  * Lint a native Galaxy workflow (.ga format).
  * Returns structured lint results with errors and warnings.

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

@@ -1 +1 @@
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+{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/workflow/lint.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAQH,OAAO,EAAe,KAAK,UAAU,EAAE,MAAM,cAAc,CAAC;AAG5D,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,cAAc,CAAC;AAqNtB;;;GAGG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU5E;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU7E;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAG9E;AA6HD;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAY1F;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAyBzF"}

package/dist/workflow/lint.js

@@ -1,40 +1,16 @@
 /**
  * Workflow linting — structural checks and best-practice warnings.
  *
- * Port of gxformat2's lint.py + linting.py. Checks workflow structure,
- * output labels, step errors, tool references, output source resolution,
- * input default types, and report markdown.
+ * Port of gxformat2's lint.py. Emission primitives live in `linting.ts`
+ * (LintContext / LintMessage / Linter base); rule classes in `lint-rules.ts`.
  */
 import { normalizedFormat2 } from "./normalized/format2.js";
 import { normalizedNative } from "./normalized/native.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
 import { detectFormat } from "./detect-format.js";
-// ---------------------------------------------------------------------------
-// LintContext — tracks errors and warnings during linting
-// ---------------------------------------------------------------------------
-export class LintContext {
-    errors = [];
-    warnings = [];
-    _prefix;
-    constructor(prefix = "") {
-        this._prefix = prefix;
-    }
-    error(message) {
-        this.errors.push(`${this._prefix}${message}`);
-    }
-    warn(message) {
-        this.warnings.push(`${this._prefix}${message}`);
-    }
-    child(prefix) {
-        const fullPrefix = this._prefix ? `${this._prefix.slice(0, -1)} > ${prefix}] ` : `[${prefix}] `;
-        const ctx = new LintContext();
-        ctx._prefix = fullPrefix;
-        // Share message arrays with parent
-        ctx.errors = this.errors;
-        ctx.warnings = this.warnings;
-        return ctx;
-    }
-}
+import { LintContext } from "./linting.js";
+import { NativeStepKeyNotInteger } from "./lint-rules.js";
+export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, } from "./linting.js";
 function toLintResult(ctx) {
     return {
         errors: ctx.errors,
@@ -92,7 +68,10 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
     let foundOutputWithoutLabel = false;
     for (const [orderIndex, step] of Object.entries(nnw.steps)) {
         if (!/^\d+$/.test(orderIndex)) {
-            ctx.error(`expected step_key to be integer not [${orderIndex}]`);
+            ctx.error(`expected step_key to be integer not [${orderIndex}]`, {
+                linter: NativeStepKeyNotInteger,
+                json_pointer: `/steps/${orderIndex}`,
+            });
         }
         for (const wo of step.workflow_outputs) {
             foundOutputs = true;

package/dist/workflow/lint.js.map

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package/dist/workflow/lint_profiles.yml

@@ -0,0 +1,41 @@
+# Lint profile catalog.
+#
+# Profiles group lint-rule IDs into named sets. Profiles apply only to
+# lint rules (schema rules always run as part of validate_*). Unknown IDs
+# are tolerated by the loader; audit tooling can flag them.
+#
+# Rule IDs mirror the ``Linter`` class names in gxformat2/lint_rules.py.
+
+structural:
+  description: "Checks that prevent execution or indicate structural breakage."
+  rules:
+    - NativeStepKeyNotInteger
+    - StepExportError
+    - StepUsesTestToolshed
+    - WorkflowHasNoOutputs
+    - WorkflowOutputMissingLabel
+    - OutputSourceNotFound
+    - InputDefaultTypeInvalid
+    - ReportMarkdownInvalid
+
+best-practices:
+  description: "Deviations from recommended authoring practice."
+  rules:
+    - WorkflowMissingAnnotation
+    - WorkflowMissingCreator
+    - WorkflowMissingLicense
+    - CreatorIdentifierNotURI
+    - StepMissingLabel
+    - StepMissingAnnotation
+    - StepInputDisconnected
+    - StepToolStateUntypedParameter
+    - StepPJAUntypedParameter
+    - TrainingWorkflowMissingTag
+    - TrainingWorkflowWrongTopic
+    - TrainingWorkflowMissingDoc
+    - TrainingWorkflowEmptyDoc
+
+release:
+  description: "Additional gates for workflows being released."
+  rules:
+    - WorkflowMissingRelease

package/dist/workflow/linting.d.ts

@@ -0,0 +1,54 @@
+/**
+ * Generic linting primitives — port of gxformat2/linting.py.
+ *
+ * `LintMessage` is a structured emission carrying prose plus `level`,
+ * `linter`, and `json_pointer` metadata. Field names are snake_case for
+ * sync-clean diff with Python. `toString()` returns the prose so template
+ * interpolation (`${m}`) and existing string-based callers keep working.
+ */
+export type LintLevel = "error" | "warn";
+export declare const LEVEL_ERROR: LintLevel;
+export declare const LEVEL_WARN: LintLevel;
+export declare class LintMessage {
+    readonly message: string;
+    readonly level: LintLevel;
+    readonly linter: string | null;
+    readonly json_pointer: string;
+    constructor(message: string, options?: {
+        level?: LintLevel;
+        linter?: string | null;
+        json_pointer?: string;
+    });
+    toString(): string;
+}
+/**
+ * Metadata-only base for lint rules. Subclasses carry class-level metadata;
+ * emission happens via `LintContext.error`/`warn` with `linter=Subclass`.
+ */
+export declare abstract class Linter {
+    static severity: "error" | "warning";
+    static applies_to: readonly ("format2" | "native")[];
+    static profile: string;
+}
+export type LinterRef = typeof Linter | string | null;
+export interface EmitOptions {
+    linter?: LinterRef;
+    json_pointer?: string;
+}
+export declare class LintContext {
+    errors: LintMessage[];
+    warnings: LintMessage[];
+    private _pointer;
+    constructor(pointer?: string);
+    error(message: string, options?: EmitOptions): void;
+    warn(message: string, options?: EmitOptions): void;
+    child(segment: string | number): LintContext;
+    private _emit;
+}
+export interface LintResult {
+    errors: LintMessage[];
+    warnings: LintMessage[];
+    error_count: number;
+    warn_count: number;
+}
+//# sourceMappingURL=linting.d.ts.map

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

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

@@ -0,0 +1,71 @@
+/**
+ * Generic linting primitives — port of gxformat2/linting.py.
+ *
+ * `LintMessage` is a structured emission carrying prose plus `level`,
+ * `linter`, and `json_pointer` metadata. Field names are snake_case for
+ * sync-clean diff with Python. `toString()` returns the prose so template
+ * interpolation (`${m}`) and existing string-based callers keep working.
+ */
+export const LEVEL_ERROR = "error";
+export const LEVEL_WARN = "warn";
+export class LintMessage {
+    message;
+    level;
+    linter;
+    json_pointer;
+    constructor(message, options = {}) {
+        this.message = message;
+        this.level = options.level ?? LEVEL_WARN;
+        this.linter = options.linter ?? null;
+        this.json_pointer = options.json_pointer ?? "";
+    }
+    toString() {
+        return this.message;
+    }
+}
+/**
+ * Metadata-only base for lint rules. Subclasses carry class-level metadata;
+ * emission happens via `LintContext.error`/`warn` with `linter=Subclass`.
+ */
+export class Linter {
+    static severity = "warning";
+    static applies_to = [];
+    static profile = "structural";
+}
+function resolveLinterName(linter) {
+    if (linter == null)
+        return null;
+    if (typeof linter === "string")
+        return linter;
+    return linter.name;
+}
+function escapePointerSegment(segment) {
+    return String(segment).replace(/~/g, "~0").replace(/\//g, "~1");
+}
+export class LintContext {
+    errors = [];
+    warnings = [];
+    _pointer;
+    constructor(pointer = "") {
+        this._pointer = pointer;
+    }
+    error(message, options = {}) {
+        this._emit(this.errors, LEVEL_ERROR, message, options);
+    }
+    warn(message, options = {}) {
+        this._emit(this.warnings, LEVEL_WARN, message, options);
+    }
+    child(segment) {
+        const newPointer = `${this._pointer}/${escapePointerSegment(segment)}`;
+        const ctx = new LintContext(newPointer);
+        ctx.errors = this.errors;
+        ctx.warnings = this.warnings;
+        return ctx;
+    }
+    _emit(target, level, message, options) {
+        const pointer = options.json_pointer !== undefined ? options.json_pointer : this._pointer;
+        const linter = resolveLinterName(options.linter);
+        target.push(new LintMessage(message, { level, linter, json_pointer: pointer }));
+    }
+}
+//# sourceMappingURL=linting.js.map

package/dist/workflow/linting.js.map

@@ -0,0 +1 @@
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package/dist/workflow/normalized/index.d.ts

@@ -1,7 +1,10 @@
 export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, 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 } from "./toFormat2.js";
-export { toNative } from "./toNative.js";
+export { toFormat2, type ToFormat2Options, type Format2StateOverride } from "./toFormat2.js";
+export { toNative, type ToNativeOptions } from "./toNative.js";
+export { toFormat2Stateful, type StepConversionStatus, type StatefulExportResult, type ToolInputsResolver, } from "./toFormat2Stateful.js";
+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 { flattenCommentData, unflattenCommentData } from "./comments.js";

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

@@ -1 +1 @@
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package/dist/workflow/normalized/index.js

@@ -2,6 +2,8 @@ export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2St
 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 { flattenCommentData, unflattenCommentData } from "./comments.js";

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

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

@@ -0,0 +1,82 @@
+/**
+ * Shared per-step runner for stateful conversions.
+ *
+ * Both `toFormat2Stateful` and `toNativeStateful` need the same boilerplate:
+ * eligibility gate → id resolution → tool-inputs lookup → optional precheck
+ * → optional pre-conversion validation → convert → optional post-conversion
+ * validation → per-step status tracking. This module factors that out so
+ * each wrapper only supplies the config that differs (predicate, id
+ * extractor, convert, optional hooks).
+ *
+ * Tool lookup is callback-shaped (matching gxformat2's
+ * `ConversionOptions.state_encode_to_*` design) — callers pass a resolver
+ * `(toolId, toolVersion) => ToolParameterModel[] | undefined` and own the
+ * caching / loading strategy. Version disambiguation is the caller's
+ * responsibility, not the runner's.
+ *
+ * Failure classes allow callers to distinguish *why* a step fell back:
+ *
+ * - `unknown_tool`    — resolver returned undefined (not in cache, no tool_id)
+ * - `precheck`        — legacy replacement params or legacy encoding detected
+ * - `pre_validation`  — native state fails `workflow_step_native` schema
+ * - `conversion`      — walker/convert threw (unknown param type, bad structure)
+ * - `post_validation` — converted format2/native state fails schema
+ */
+import type { ToolParameterModel } from "../../schema/bundle-types.js";
+export type ToolInputsResolver = (toolId: string, toolVersion: string | null) => ToolParameterModel[] | undefined;
+export type StepConversionFailureClass = "unknown_tool" | "precheck" | "pre_validation" | "conversion" | "post_validation";
+export interface StepConversionStatus {
+    stepId: string;
+    toolId?: string;
+    toolVersion?: string | null;
+    converted: boolean;
+    /** Present when converted=false. Distinguishes why the fallback happened. */
+    failureClass?: StepConversionFailureClass;
+    error?: string;
+}
+export interface StepRunnerConfig<Args, Result> {
+    /** Resolve parameter inputs for a given tool_id/tool_version pair. */
+    toolInputsResolver: ToolInputsResolver;
+    /** Per-step status entries are pushed into this array. */
+    status: StepConversionStatus[];
+    /** Return true if the step should participate in stateful conversion. */
+    isEligible: (args: Args) => boolean;
+    /** Extract identifiers for status reporting and lookup. */
+    resolveIds: (args: Args) => {
+        stepId: string;
+        toolId?: string;
+        toolVersion?: string | null;
+    };
+    /**
+     * Optional non-throwing precheck. Return an array of reasons (strings)
+     * if the step should be skipped without attempting conversion; return
+     * null/empty for "ok to proceed".
+     */
+    precheck?: (args: Args, inputs: ToolParameterModel[]) => string[] | null;
+    /**
+     * Optional pre-conversion validation. Throw to signal failure — the
+     * runner will catch, classify as `pre_validation`, and fall back.
+     */
+    preValidate?: (args: Args, inputs: ToolParameterModel[]) => void;
+    /** Perform the conversion. Thrown errors are classified as `conversion`. */
+    convert: (args: Args, inputs: ToolParameterModel[]) => Result;
+    /**
+     * Optional post-conversion validation on the converted result. Throw to
+     * signal failure — classified as `post_validation`, result discarded.
+     */
+    postValidate?: (result: Result, inputs: ToolParameterModel[]) => void;
+}
+/**
+ * Build a per-step callback with status tracking and graceful fallback.
+ *
+ * Return semantics:
+ * - ineligible step → `null`, no status entry
+ * - resolver returned undefined → `null`, `unknown_tool` status
+ * - precheck returned reasons → `null`, `precheck` status
+ * - preValidate threw → `null`, `pre_validation` status
+ * - convert threw → `null`, `conversion` status
+ * - postValidate threw → `null`, `post_validation` status
+ * - success → result, `converted: true` status
+ */
+export declare function makeStepConversionRunner<Args, Result>(config: StepRunnerConfig<Args, Result>): (args: Args) => Result | null;
+//# sourceMappingURL=stateful-runner.d.ts.map

package/dist/workflow/normalized/stateful-runner.d.ts.map

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

@@ -0,0 +1,122 @@
+/**
+ * Shared per-step runner for stateful conversions.
+ *
+ * Both `toFormat2Stateful` and `toNativeStateful` need the same boilerplate:
+ * eligibility gate → id resolution → tool-inputs lookup → optional precheck
+ * → optional pre-conversion validation → convert → optional post-conversion
+ * validation → per-step status tracking. This module factors that out so
+ * each wrapper only supplies the config that differs (predicate, id
+ * extractor, convert, optional hooks).
+ *
+ * Tool lookup is callback-shaped (matching gxformat2's
+ * `ConversionOptions.state_encode_to_*` design) — callers pass a resolver
+ * `(toolId, toolVersion) => ToolParameterModel[] | undefined` and own the
+ * caching / loading strategy. Version disambiguation is the caller's
+ * responsibility, not the runner's.
+ *
+ * Failure classes allow callers to distinguish *why* a step fell back:
+ *
+ * - `unknown_tool`    — resolver returned undefined (not in cache, no tool_id)
+ * - `precheck`        — legacy replacement params or legacy encoding detected
+ * - `pre_validation`  — native state fails `workflow_step_native` schema
+ * - `conversion`      — walker/convert threw (unknown param type, bad structure)
+ * - `post_validation` — converted format2/native state fails schema
+ */
+/**
+ * Build a per-step callback with status tracking and graceful fallback.
+ *
+ * Return semantics:
+ * - ineligible step → `null`, no status entry
+ * - resolver returned undefined → `null`, `unknown_tool` status
+ * - precheck returned reasons → `null`, `precheck` status
+ * - preValidate threw → `null`, `pre_validation` status
+ * - convert threw → `null`, `conversion` status
+ * - postValidate threw → `null`, `post_validation` status
+ * - success → result, `converted: true` status
+ */
+export function makeStepConversionRunner(config) {
+    const { toolInputsResolver, status, isEligible, resolveIds, precheck, preValidate, convert, postValidate, } = config;
+    return (args) => {
+        if (!isEligible(args))
+            return null;
+        const { stepId, toolId, toolVersion = null } = resolveIds(args);
+        const inputs = toolId != null ? toolInputsResolver(toolId, toolVersion) : undefined;
+        if (inputs == null) {
+            status.push({
+                stepId,
+                toolId,
+                toolVersion,
+                converted: false,
+                failureClass: "unknown_tool",
+                error: toolId == null
+                    ? "step has no tool_id"
+                    : `tool not resolved: ${toolId}${toolVersion ? `@${toolVersion}` : ""}`,
+            });
+            return null;
+        }
+        if (precheck) {
+            const reasons = precheck(args, inputs);
+            if (reasons && reasons.length > 0) {
+                status.push({
+                    stepId,
+                    toolId,
+                    toolVersion,
+                    converted: false,
+                    failureClass: "precheck",
+                    error: reasons.join("; "),
+                });
+                return null;
+            }
+        }
+        if (preValidate) {
+            try {
+                preValidate(args, inputs);
+            }
+            catch (err) {
+                status.push({
+                    stepId,
+                    toolId,
+                    toolVersion,
+                    converted: false,
+                    failureClass: "pre_validation",
+                    error: err instanceof Error ? err.message : String(err),
+                });
+                return null;
+            }
+        }
+        let result;
+        try {
+            result = convert(args, inputs);
+        }
+        catch (err) {
+            status.push({
+                stepId,
+                toolId,
+                toolVersion,
+                converted: false,
+                failureClass: "conversion",
+                error: err instanceof Error ? err.message : String(err),
+            });
+            return null;
+        }
+        if (postValidate) {
+            try {
+                postValidate(result, inputs);
+            }
+            catch (err) {
+                status.push({
+                    stepId,
+                    toolId,
+                    toolVersion,
+                    converted: false,
+                    failureClass: "post_validation",
+                    error: err instanceof Error ? err.message : String(err),
+                });
+                return null;
+            }
+        }
+        status.push({ stepId, toolId, toolVersion, converted: true });
+        return result;
+    };
+}
+//# sourceMappingURL=stateful-runner.js.map

package/dist/workflow/normalized/stateful-runner.js.map

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

@@ -3,9 +3,27 @@
  *
  * Port of gxformat2/normalized/_conversion.py to_format2 + helpers.
  */
+import type { NormalizedNativeStep } from "./native.js";
 import type { NormalizedFormat2Workflow } from "./format2.js";
+/**
+ * Per-step callback result: a replacement format2 state dict + optional `in`
+ * block overrides (flat path → source). Return null to fall back to the
+ * default schema-free passthrough for this step.
+ */
+export interface Format2StateOverride {
+    state: Record<string, unknown>;
+    in?: Record<string, string>;
+}
+export interface ToFormat2Options {
+    /**
+     * Per-step callback: given the native step, return a replacement format2
+     * `state` dict (and optional `in` block additions), or null for the default
+     * passthrough behavior.
+     */
+    stateEncodeToFormat2?: (nativeStep: NormalizedNativeStep) => Format2StateOverride | null;
+}
 /**
  * Convert a native Galaxy workflow to normalized Format2.
  */
-export declare function toFormat2(raw: unknown): NormalizedFormat2Workflow;
+export declare function toFormat2(raw: unknown, options?: ToFormat2Options): NormalizedFormat2Workflow;
 //# sourceMappingURL=toFormat2.d.ts.map