@galaxy-tool-util/schema 1.10.0 → 1.12.0

package/dist/schema/parsed-tool.js

@@ -62,10 +62,64 @@ export const ToolOutputCollectionStructure = S.Struct({
     structured_like: S.NullOr(S.String),
     discover_datasets: S.NullOr(S.Array(DatasetCollectionDescription)),
 });
-export const ToolOutputCollection = S.Struct({
+/**
+ * Canonical (flat) collection-output shape — Galaxy's tool_parsing_abstraction
+ * model and the TS parsers carry the structure fields at the output's top level.
+ * `ToolOutputCollectionStructure` stays the shared building block the parsers
+ * assemble before spreading it flat.
+ */
+const ToolOutputCollectionFlat = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("collection"),
+    ...ToolOutputCollectionStructure.fields,
+});
+/**
+ * Decode input for a collection output. Accepts either the flat fields or a
+ * legacy nested `structure` wrapper (which current Galaxy releases still emit),
+ * so the port decodes `ParsedTool` JSON from any Galaxy version.
+ */
+const ToolOutputCollectionEncoded = S.Struct({
     ...ToolOutputBase.fields,
     type: S.Literal("collection"),
-    structure: ToolOutputCollectionStructure,
+    collection_type: S.optional(S.NullOr(S.String)),
+    collection_type_source: S.optional(S.NullOr(S.String)),
+    collection_type_from_rules: S.optional(S.NullOr(S.String)),
+    structured_like: S.optional(S.NullOr(S.String)),
+    discover_datasets: S.optional(S.NullOr(S.Array(DatasetCollectionDescription))),
+    structure: S.optional(ToolOutputCollectionStructure),
+});
+/**
+ * Decode-tolerant collection output: a nested `structure` is lifted to the top
+ * level, so both shapes decode to the flat form. Encode always emits flat — the
+ * canonical shape the parsers produce.
+ */
+export const ToolOutputCollection = S.transform(ToolOutputCollectionEncoded, ToolOutputCollectionFlat, {
+    strict: false,
+    decode: (o) => {
+        const s = o.structure;
+        return {
+            name: o.name,
+            label: o.label,
+            hidden: o.hidden,
+            type: "collection",
+            collection_type: o.collection_type ?? s?.collection_type ?? null,
+            collection_type_source: o.collection_type_source ?? s?.collection_type_source ?? null,
+            collection_type_from_rules: o.collection_type_from_rules ?? s?.collection_type_from_rules ?? null,
+            structured_like: o.structured_like ?? s?.structured_like ?? null,
+            discover_datasets: o.discover_datasets ?? s?.discover_datasets ?? null,
+        };
+    },
+    encode: (o) => ({
+        name: o.name,
+        label: o.label,
+        hidden: o.hidden,
+        type: "collection",
+        collection_type: o.collection_type,
+        collection_type_source: o.collection_type_source,
+        collection_type_from_rules: o.collection_type_from_rules,
+        structured_like: o.structured_like,
+        discover_datasets: o.discover_datasets,
+    }),
 });
 export const ToolOutputText = S.Struct({
     ...ToolOutputBase.fields,

package/dist/schema/parsed-tool.js.map

@@ -1 +1 @@
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package/dist/schema/state-representations.js

@@ -43,7 +43,7 @@ export function allowsConnectedOrRuntimeValue(rep) {
     return rep === "workflow_step_native";
 }
 export function allOptional(rep) {
-    return rep === "landing_request" || rep === "landing_request_internal";
+    return rep === "landing_request" || rep === "landing_request_internal" || rep === "workflow_step";
 }
 export function isWorkflowStep(rep) {
     return (rep === "workflow_step" || rep === "workflow_step_linked" || rep === "workflow_step_native");

package/dist/schema/state-representations.js.map

@@ -1 +1 @@
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package/dist/tool-state-validator.d.ts

@@ -16,7 +16,7 @@ export declare class ToolStateValidator {
     private readonly toolInfo;
     constructor(toolInfo: ToolInfoLookup);
     validateNativeStep(toolId: string, toolVersion: string | null, toolState: Record<string, unknown>, inputConnections?: Record<string, unknown>): Promise<ToolStateDiagnostic[]>;
-    validateFormat2Step(toolId: string, toolVersion: string | null, format2State: Record<string, unknown>): Promise<ToolStateDiagnostic[]>;
+    validateFormat2Step(toolId: string, toolVersion: string | null, format2State: Record<string, unknown>, inputConnections?: Record<string, unknown>): Promise<ToolStateDiagnostic[]>;
     /**
      * Strict variant: reports unknown parameter keys as diagnostics.
      *
@@ -25,6 +25,6 @@ export declare class ToolStateValidator {
      * where unknown params should be flagged. Returns structured diagnostics
      * with dot-separated paths so callers can locate issues in the YAML AST.
      */
-    validateFormat2StepStrict(toolId: string, toolVersion: string | null, format2State: Record<string, unknown>): Promise<ToolStateDiagnostic[]>;
+    validateFormat2StepStrict(toolId: string, toolVersion: string | null, format2State: Record<string, unknown>, inputConnections?: Record<string, unknown>): Promise<ToolStateDiagnostic[]>;
 }
 //# sourceMappingURL=tool-state-validator.d.ts.map

package/dist/tool-state-validator.d.ts.map

@@ -1 +1 @@
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package/dist/tool-state-validator.js

@@ -28,13 +28,13 @@ export class ToolStateValidator {
             throw e;
         }
     }
-    async validateFormat2Step(toolId, toolVersion, format2State) {
+    async validateFormat2Step(toolId, toolVersion, format2State, inputConnections = {}) {
         const parsed = await this.toolInfo.getToolInfo(toolId, toolVersion).catch(() => null);
         if (!parsed)
             return [];
         const inputs = parsed.inputs;
         try {
-            validateFormat2StepState(inputs, format2State);
+            validateFormat2StepState(inputs, format2State, inputConnections);
             return [];
         }
         catch (e) {
@@ -55,12 +55,12 @@ export class ToolStateValidator {
      * where unknown params should be flagged. Returns structured diagnostics
      * with dot-separated paths so callers can locate issues in the YAML AST.
      */
-    async validateFormat2StepStrict(toolId, toolVersion, format2State) {
+    async validateFormat2StepStrict(toolId, toolVersion, format2State, inputConnections = {}) {
         const parsed = await this.toolInfo.getToolInfo(toolId, toolVersion).catch(() => null);
         if (!parsed)
             return [];
         const inputs = parsed.inputs;
-        return validateFormat2StepStateStrict(inputs, format2State);
+        return validateFormat2StepStateStrict(inputs, format2State, inputConnections);
     }
 }
 //# sourceMappingURL=tool-state-validator.js.map

package/dist/tool-state-validator.js.map

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package/dist/trs/index.d.ts

@@ -0,0 +1,110 @@
+/**
+ * GA4GH TRS (Tool Registry Service) v2 schemas.
+ *
+ * Hand-port of the subset of the TRS OpenAPI consumed by Galaxy's tool
+ * shed surface — see `lib/tool_shed_client/schema/trs.py` upstream. Only
+ * the types referenced from `Tool`/`ToolVersion` are included.
+ */
+import * as S from "effect/Schema";
+export declare const ImageType: S.Literal<["Docker", "Singularity", "Conda"]>;
+export type ImageType = S.Schema.Type<typeof ImageType>;
+export declare const DescriptorType: S.Literal<["CWL", "WDL", "NFL", "GALAXY", "SMK"]>;
+export type DescriptorType = S.Schema.Type<typeof DescriptorType>;
+export declare const FileType: S.Literal<["TEST_FILE", "PRIMARY_DESCRIPTOR", "SECONDARY_DESCRIPTOR", "CONTAINERFILE", "OTHER"]>;
+export type FileType = S.Schema.Type<typeof FileType>;
+export declare const Checksum: S.Struct<{
+    checksum: typeof S.String;
+    type: typeof S.String;
+}>;
+export type Checksum = S.Schema.Type<typeof Checksum>;
+export declare const ImageData: S.Struct<{
+    registry_host: S.optional<typeof S.String>;
+    image_name: S.optional<typeof S.String>;
+    size: S.optional<typeof S.Number>;
+    updated: S.optional<typeof S.String>;
+    checksum: S.optional<S.Array$<S.Struct<{
+        checksum: typeof S.String;
+        type: typeof S.String;
+    }>>>;
+    image_type: S.optional<S.Literal<["Docker", "Singularity", "Conda"]>>;
+}>;
+export type ImageData = S.Schema.Type<typeof ImageData>;
+export declare const ToolClass: S.Struct<{
+    id: S.optional<typeof S.String>;
+    name: S.optional<typeof S.String>;
+    description: S.optional<typeof S.String>;
+}>;
+export type ToolClass = S.Schema.Type<typeof ToolClass>;
+export declare const ToolVersion: S.Struct<{
+    url: typeof S.String;
+    id: typeof S.String;
+    author: S.optional<S.Array$<typeof S.String>>;
+    name: S.optional<typeof S.String>;
+    is_production: S.optional<typeof S.Boolean>;
+    images: S.optional<S.Array$<S.Struct<{
+        registry_host: S.optional<typeof S.String>;
+        image_name: S.optional<typeof S.String>;
+        size: S.optional<typeof S.Number>;
+        updated: S.optional<typeof S.String>;
+        checksum: S.optional<S.Array$<S.Struct<{
+            checksum: typeof S.String;
+            type: typeof S.String;
+        }>>>;
+        image_type: S.optional<S.Literal<["Docker", "Singularity", "Conda"]>>;
+    }>>>;
+    descriptor_type: S.optional<S.Array$<S.Literal<["CWL", "WDL", "NFL", "GALAXY", "SMK"]>>>;
+    descriptor_type_version: S.optional<S.Record$<typeof S.String, S.Array$<typeof S.String>>>;
+    containerfile: S.optional<typeof S.Boolean>;
+    meta_version: S.optional<typeof S.String>;
+    verified: S.optional<typeof S.Boolean>;
+    verified_source: S.optional<S.Array$<typeof S.String>>;
+    signed: S.optional<typeof S.Boolean>;
+    included_apps: S.optional<S.Array$<typeof S.String>>;
+}>;
+export type ToolVersion = S.Schema.Type<typeof ToolVersion>;
+export declare const Tool: S.Struct<{
+    url: typeof S.String;
+    id: typeof S.String;
+    organization: typeof S.String;
+    toolclass: S.Struct<{
+        id: S.optional<typeof S.String>;
+        name: S.optional<typeof S.String>;
+        description: S.optional<typeof S.String>;
+    }>;
+    versions: S.Array$<S.Struct<{
+        url: typeof S.String;
+        id: typeof S.String;
+        author: S.optional<S.Array$<typeof S.String>>;
+        name: S.optional<typeof S.String>;
+        is_production: S.optional<typeof S.Boolean>;
+        images: S.optional<S.Array$<S.Struct<{
+            registry_host: S.optional<typeof S.String>;
+            image_name: S.optional<typeof S.String>;
+            size: S.optional<typeof S.Number>;
+            updated: S.optional<typeof S.String>;
+            checksum: S.optional<S.Array$<S.Struct<{
+                checksum: typeof S.String;
+                type: typeof S.String;
+            }>>>;
+            image_type: S.optional<S.Literal<["Docker", "Singularity", "Conda"]>>;
+        }>>>;
+        descriptor_type: S.optional<S.Array$<S.Literal<["CWL", "WDL", "NFL", "GALAXY", "SMK"]>>>;
+        descriptor_type_version: S.optional<S.Record$<typeof S.String, S.Array$<typeof S.String>>>;
+        containerfile: S.optional<typeof S.Boolean>;
+        meta_version: S.optional<typeof S.String>;
+        verified: S.optional<typeof S.Boolean>;
+        verified_source: S.optional<S.Array$<typeof S.String>>;
+        signed: S.optional<typeof S.Boolean>;
+        included_apps: S.optional<S.Array$<typeof S.String>>;
+    }>>;
+    aliases: S.optional<S.Array$<typeof S.String>>;
+    name: S.optional<typeof S.String>;
+    description: S.optional<typeof S.String>;
+    meta_version: S.optional<typeof S.String>;
+    has_checker: S.optional<typeof S.Boolean>;
+    checker_url: S.optional<typeof S.String>;
+}>;
+export type Tool = S.Schema.Type<typeof Tool>;
+/** Galaxy's default tool class — single hardcoded value. */
+export declare const GALAXY_TOOL_CLASS: ToolClass;
+//# sourceMappingURL=index.d.ts.map

package/dist/trs/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/trs/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AAEnC,eAAO,MAAM,SAAS,+CAA8C,CAAC;AACrE,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,SAAS,CAAC,CAAC;AAExD,eAAO,MAAM,cAAc,mDAAkD,CAAC;AAC9E,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,cAAc,CAAC,CAAC;AAElE,eAAO,MAAM,QAAQ,kGAMpB,CAAC;AACF,MAAM,MAAM,QAAQ,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,QAAQ,CAAC,CAAC;AAEtD,eAAO,MAAM,QAAQ;;;EAGnB,CAAC;AACH,MAAM,MAAM,QAAQ,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,QAAQ,CAAC,CAAC;AAEtD,eAAO,MAAM,SAAS;;;;;;;;;;EAOpB,CAAC;AACH,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,SAAS,CAAC,CAAC;AAExD,eAAO,MAAM,SAAS;;;;EAIpB,CAAC;AACH,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,SAAS,CAAC,CAAC;AAExD,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;EAetB,CAAC;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,WAAW,CAAC,CAAC;AAE5D,eAAO,MAAM,IAAI;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAYf,CAAC;AACH,MAAM,MAAM,IAAI,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,IAAI,CAAC,CAAC;AAE9C,4DAA4D;AAC5D,eAAO,MAAM,iBAAiB,EAAE,SAI/B,CAAC"}

package/dist/trs/index.js

@@ -0,0 +1,64 @@
+/**
+ * GA4GH TRS (Tool Registry Service) v2 schemas.
+ *
+ * Hand-port of the subset of the TRS OpenAPI consumed by Galaxy's tool
+ * shed surface — see `lib/tool_shed_client/schema/trs.py` upstream. Only
+ * the types referenced from `Tool`/`ToolVersion` are included.
+ */
+import * as S from "effect/Schema";
+export const ImageType = S.Literal("Docker", "Singularity", "Conda");
+export const DescriptorType = S.Literal("CWL", "WDL", "NFL", "GALAXY", "SMK");
+export const FileType = S.Literal("TEST_FILE", "PRIMARY_DESCRIPTOR", "SECONDARY_DESCRIPTOR", "CONTAINERFILE", "OTHER");
+export const Checksum = S.Struct({
+    checksum: S.String,
+    type: S.String,
+});
+export const ImageData = S.Struct({
+    registry_host: S.optional(S.String),
+    image_name: S.optional(S.String),
+    size: S.optional(S.Number),
+    updated: S.optional(S.String),
+    checksum: S.optional(S.Array(Checksum)),
+    image_type: S.optional(ImageType),
+});
+export const ToolClass = S.Struct({
+    id: S.optional(S.String),
+    name: S.optional(S.String),
+    description: S.optional(S.String),
+});
+export const ToolVersion = S.Struct({
+    url: S.String,
+    id: S.String,
+    author: S.optional(S.Array(S.String)),
+    name: S.optional(S.String),
+    is_production: S.optional(S.Boolean),
+    images: S.optional(S.Array(ImageData)),
+    descriptor_type: S.optional(S.Array(DescriptorType)),
+    descriptor_type_version: S.optional(S.Record({ key: S.String, value: S.Array(S.String) })),
+    containerfile: S.optional(S.Boolean),
+    meta_version: S.optional(S.String),
+    verified: S.optional(S.Boolean),
+    verified_source: S.optional(S.Array(S.String)),
+    signed: S.optional(S.Boolean),
+    included_apps: S.optional(S.Array(S.String)),
+});
+export const Tool = S.Struct({
+    url: S.String,
+    id: S.String,
+    organization: S.String,
+    toolclass: ToolClass,
+    versions: S.Array(ToolVersion),
+    aliases: S.optional(S.Array(S.String)),
+    name: S.optional(S.String),
+    description: S.optional(S.String),
+    meta_version: S.optional(S.String),
+    has_checker: S.optional(S.Boolean),
+    checker_url: S.optional(S.String),
+});
+/** Galaxy's default tool class — single hardcoded value. */
+export const GALAXY_TOOL_CLASS = {
+    id: "GalaxyTool",
+    name: "Galaxy Tool",
+    description: "Galaxy XML/YAML tool definition.",
+};
+//# sourceMappingURL=index.js.map

package/dist/trs/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/trs/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AAEnC,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAC,OAAO,CAAC,QAAQ,EAAE,aAAa,EAAE,OAAO,CAAC,CAAC;AAGrE,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;AAG9E,MAAM,CAAC,MAAM,QAAQ,GAAG,CAAC,CAAC,OAAO,CAC/B,WAAW,EACX,oBAAoB,EACpB,sBAAsB,EACtB,eAAe,EACf,OAAO,CACR,CAAC;AAGF,MAAM,CAAC,MAAM,QAAQ,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,QAAQ,EAAE,CAAC,CAAC,MAAM;IAClB,IAAI,EAAE,CAAC,CAAC,MAAM;CACf,CAAC,CAAC;AAGH,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAC,MAAM,CAAC;IAChC,aAAa,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IACnC,UAAU,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAChC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAC1B,OAAO,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAC7B,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IACvC,UAAU,EAAE,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC;CAClC,CAAC,CAAC;AAGH,MAAM,CAAC,MAAM,SAAS,GAAG,CAAC,CAAC,MAAM,CAAC;IAChC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IACxB,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAC1B,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;CAClC,CAAC,CAAC;AAGH,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,GAAG,EAAE,CAAC,CAAC,MAAM;IACb,EAAE,EAAE,CAAC,CAAC,MAAM;IACZ,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAC1B,aAAa,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC;IACpC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;IACtC,eAAe,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;IACpD,uBAAuB,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IAC1F,aAAa,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC;IACpC,YAAY,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAClC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC;IAC/B,eAAe,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC;IAC7B,aAAa,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;CAC7C,CAAC,CAAC;AAGH,MAAM,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,GAAG,EAAE,CAAC,CAAC,MAAM;IACb,EAAE,EAAE,CAAC,CAAC,MAAM;IACZ,YAAY,EAAE,CAAC,CAAC,MAAM;IACtB,SAAS,EAAE,SAAS;IACpB,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC;IAC9B,OAAO,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;IACtC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAC1B,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IACjC,YAAY,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;IAClC,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC;IAClC,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC;CAClC,CAAC,CAAC;AAGH,4DAA4D;AAC5D,MAAM,CAAC,MAAM,iBAAiB,GAAc;IAC1C,EAAE,EAAE,YAAY;IAChB,IAAI,EAAE,aAAa;IACnB,WAAW,EAAE,kCAAkC;CAChD,CAAC"}

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

@@ -8,5 +8,8 @@
  * containers are intentionally out of scope — they're not on the TS
  * `ParsedTool` shape consumers depend on.
  */
-export { parseInlineTool, type InlineRepresentation } from "./parse.js";
+export { parseInlineTool, parseYamlTool, type InlineRepresentation, type YamlToolRepresentation, } from "./parse.js";
+export { parseInputs, inputModelsForPage } from "./inputs.js";
+export { parseOutputs, parseDiscoverDatasets } from "./outputs.js";
+export { DictInputSource, DictPageSource, type InputSource, type PageSource, type InputType, } from "./input-source.js";
 //# sourceMappingURL=index.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,EAAE,eAAe,EAAE,KAAK,oBAAoB,EAAE,MAAM,YAAY,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,EACL,eAAe,EACf,aAAa,EACb,KAAK,oBAAoB,EACzB,KAAK,sBAAsB,GAC5B,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,WAAW,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AAC9D,OAAO,EAAE,YAAY,EAAE,qBAAqB,EAAE,MAAM,cAAc,CAAC;AACnE,OAAO,EACL,eAAe,EACf,cAAc,EACd,KAAK,WAAW,EAChB,KAAK,UAAU,EACf,KAAK,SAAS,GACf,MAAM,mBAAmB,CAAC"}

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

@@ -8,5 +8,8 @@
  * containers are intentionally out of scope — they're not on the TS
  * `ParsedTool` shape consumers depend on.
  */
-export { parseInlineTool } from "./parse.js";
+export { parseInlineTool, parseYamlTool, } from "./parse.js";
+export { parseInputs, inputModelsForPage } from "./inputs.js";
+export { parseOutputs, parseDiscoverDatasets } from "./outputs.js";
+export { DictInputSource, DictPageSource, } from "./input-source.js";
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/user-tool-parse/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,EAAE,eAAe,EAA6B,MAAM,YAAY,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/user-tool-parse/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,EACL,eAAe,EACf,aAAa,GAGd,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,WAAW,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AAC9D,OAAO,EAAE,YAAY,EAAE,qBAAqB,EAAE,MAAM,cAAc,CAAC;AACnE,OAAO,EACL,eAAe,EACf,cAAc,GAIf,MAAM,mBAAmB,CAAC"}

package/dist/user-tool-parse/input-source.d.ts

@@ -0,0 +1,105 @@
+/**
+ * `InputSource` / `PageSource` seam — the TS mirror of Galaxy's
+ * `galaxy.tool_util.parser.interface.InputSource` / `PageSource`. Decouples the
+ * input-tree walk (who reads the source) from the parameter-model factory in
+ * `./inputs.ts` (the `_from_input_source_galaxy` + `input_models_for_page`
+ * equivalent), so an XML-backed source in `@galaxy-tool-util/tool-xml` can feed
+ * the same factory.
+ *
+ * This module is the dependency-free interface plus the inline/YAML dict
+ * implementation (`DictInputSource` / `DictPageSource`), mirroring Galaxy's
+ * `YamlInputSource` / `YamlPageSource`. Coercion here is dict-native (native
+ * YAML bools/numbers pass through `get`; string coercion matches the previous
+ * inline reads) — it deliberately does NOT adopt XML's `string_as_bool`
+ * semantics, which live on the XML source in `tool-xml`.
+ *
+ * Only the methods the current factory consumes are on the interface. Further
+ * Galaxy accessors (dynamic options, `get_bool_or_none`, conversion tuples,
+ * sanitizers) land with the feature slices that need them.
+ */
+import type { LabelValue, DrillDownOption, ValidatorModel } from "../schema/bundle-types.js";
+/**
+ * Discriminator returned by `parseInputType`. `"section"` and `"display"` are
+ * returned only by the XML source (`tag == "section"` / `"display"`).
+ * `DictInputSource` mirrors `YamlInputSource.parse_input_type`, which maps only
+ * `repeat`/`conditional` and treats everything else (including `section`) as
+ * `"param"` — YAML sections are intentionally unsupported until Galaxy's YAML
+ * path supports them. `"display"` (data_source tools) is not a real input and is
+ * skipped by `inputModelsForPage`, matching `factory.input_models_for_page`.
+ */
+export type InputType = "param" | "conditional" | "repeat" | "section" | "display";
+export interface PageSource {
+    parseInputSources(): InputSource[];
+}
+export interface InputSource {
+    /** Raw named property (string for XML, native value for dict). */
+    get(key: string, defaultValue?: unknown): unknown;
+    /** Named property coerced to boolean. */
+    getBool(key: string, defaultValue: boolean): boolean;
+    parseInputType(): InputType;
+    parseName(): string;
+    parseLabel(): string | null;
+    parseHelp(): string | null;
+    parseOptional(defaultValue?: boolean): boolean;
+    parseExtensions(): string[];
+    /**
+     * True when a select's options are computed dynamically (e.g. a data table or
+     * `dynamic_options` code) rather than listed statically — the factory then
+     * emits `options: null`. Mirrors `parse_dynamic_options() is not None`; the
+     * inline/YAML source is always static (Galaxy's base returns `None`).
+     */
+    hasDynamicOptions(): boolean;
+    /**
+     * True when a drill-down's options come from `dynamic_options` code rather
+     * than a static `<options>` tree — the factory then emits `options: null`.
+     * Mirrors `parse_drill_down_dynamic_options() is not None`.
+     */
+    hasDrillDownDynamicOptions(): boolean;
+    /** Static `<option>` list for selects, or `null` when none are defined. */
+    parseStaticOptions(): LabelValue[] | null;
+    parseDrillDownStaticOptions(): DrillDownOption[] | null;
+    parseValidators(): ValidatorModel[];
+    /** Nested inputs for a repeat/section container. */
+    parseNestedInputsSource(): PageSource;
+    /** `test_parameter` source for a conditional. */
+    parseTestInputSource(): InputSource;
+    /** `[discriminator, page]` pairs for a conditional's whens. */
+    parseWhenInputSources(): Array<[unknown, PageSource]>;
+    parseDefault(): unknown;
+}
+type Dict = Record<string, unknown>;
+export declare class DictPageSource implements PageSource {
+    private readonly raw;
+    constructor(raw: unknown);
+    parseInputSources(): InputSource[];
+}
+export declare class DictInputSource implements InputSource {
+    private readonly input;
+    constructor(input: Dict);
+    get(key: string, defaultValue?: unknown): unknown;
+    getBool(key: string, defaultValue: boolean): boolean;
+    parseInputType(): InputType;
+    parseName(): string;
+    parseLabel(): string | null;
+    parseHelp(): string | null;
+    parseOptional(defaultValue?: boolean): boolean;
+    parseExtensions(): string[];
+    hasDynamicOptions(): boolean;
+    hasDrillDownDynamicOptions(): boolean;
+    parseStaticOptions(): LabelValue[] | null;
+    parseDrillDownStaticOptions(): DrillDownOption[] | null;
+    parseValidators(): ValidatorModel[];
+    parseNestedInputsSource(): PageSource;
+    parseTestInputSource(): InputSource;
+    parseWhenInputSources(): Array<[unknown, PageSource]>;
+    parseDefault(): unknown;
+}
+export declare function isDict(v: unknown): v is Dict;
+export declare function readString(v: unknown): string;
+export declare function readNullableString(v: unknown): string | null;
+export declare function readBool(v: unknown, fallback: boolean): boolean;
+export declare function coerceBool(v: unknown): boolean;
+export declare function readNullableInt(v: unknown): number | null;
+export declare function readNullableFloat(v: unknown): number | null;
+export {};
+//# sourceMappingURL=input-source.d.ts.map

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

@@ -0,0 +1 @@
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