@galaxy-tool-util/cli 1.10.1 → 1.13.1

package/dist/commands/validate-workflow.d.ts

@@ -22,8 +22,18 @@ export declare function decodeStructureErrors(data: Record<string, unknown>, for
 export type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
 import type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
 export declare function runValidateWorkflow(filePath: string, opts: ValidateWorkflowOptions): Promise<void>;
-export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
-export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
+/**
+ * Validate (or, when `cache` is null, merely enumerate) the tool steps of a
+ * native workflow. Passing `cache: null` skips tool resolution entirely and
+ * returns one `skip_no_tool_state` result per tool step — used by
+ * `validate-tree --no-tool-state` so the step count is still reported.
+ */
+export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache | null, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
+/**
+ * Validate (or, when `cache` is null, merely enumerate) the tool steps of a
+ * format2 workflow. See {@link validateNativeSteps} for the null-cache behavior.
+ */
+export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache | null, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
 /**
  * Detect legacy parameter encoding in workflow tool_state fields.
  *

package/dist/commands/validate-workflow.d.ts.map

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package/dist/commands/validate-workflow.js

@@ -1,4 +1,4 @@
-import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, isGalaxyUserToolRun, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
 import * as ParseResult from "effect/ParseResult";
 import * as S from "effect/Schema";
 import { dirname } from "node:path";
@@ -9,6 +9,7 @@ import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
 import { resolveStrictOptions } from "./strict-options.js";
 import { findStdoutSinkConflict, writeReportHtml } from "./report-output.js";
 import { buildConnectionReport } from "./connection-validation.js";
+import { embeddedToolDefinition, embeddedToolIdentity, isEmbeddedTool, resolveEmbeddedTool, } from "./embedded-tool.js";
 function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
     return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
@@ -125,6 +126,7 @@ export async function runValidateWorkflow(filePath, opts) {
         }
     }
     const stateOk = !results.some((r) => r.status === "fail");
+    const strictStateSkipped = strict.strictState && results.some((r) => r.status !== "ok" && r.status !== "fail");
     let connectionReport = null;
     if (opts.connections) {
         connectionReport = await buildConnectionReport(data, cache);
@@ -142,7 +144,7 @@ export async function runValidateWorkflow(filePath, opts) {
             console.log(JSON.stringify(report, null, 2));
         }
         await writeReportHtml("validate", report, opts.reportHtml);
-        process.exitCode = structOk && stateOk && connectionsOk ? 0 : 1;
+        process.exitCode = strictStateSkipped ? 2 : structOk && stateOk && connectionsOk ? 0 : 1;
         return;
     }
     if (results.length === 0) {
@@ -157,7 +159,7 @@ export async function runValidateWorkflow(filePath, opts) {
     if (connectionReport !== null)
         printConnectionReport(connectionReport);
     // --- strict state: promote skips to failures ---
-    if (strict.strictState && results.some((r) => r.status !== "ok" && r.status !== "fail")) {
+    if (strictStateSkipped) {
         console.error("Strict state: skipped steps not allowed");
         process.exitCode = 2;
         return;
@@ -187,6 +189,12 @@ function printConnectionReport(report) {
     }
 }
 // --- Native validation ---
+/**
+ * Validate (or, when `cache` is null, merely enumerate) the tool steps of a
+ * native workflow. Passing `cache: null` skips tool resolution entirely and
+ * returns one `skip_no_tool_state` result per tool step — used by
+ * `validate-tree --no-tool-state` so the step count is still reported.
+ */
 export async function validateNativeSteps(data, cache, prefix = "", expansionOpts, service) {
     const expanded = await expandedNative(data, expansionOpts);
     return _validateNativeWorkflow(expanded, cache, prefix, service);
@@ -201,6 +209,12 @@ async function _validateNativeWorkflow(wf, cache, prefix, service) {
             results.push(...subResults);
             continue;
         }
+        // An embedded definition wins over tool_id, matching connection validation.
+        const embedded = embeddedToolDefinition(step);
+        if (embedded) {
+            results.push(_validateEmbeddedNativeStep(step, stepLabel, embedded, cache));
+            continue;
+        }
         const toolId = step.tool_id;
         if (!toolId)
             continue;
@@ -211,6 +225,15 @@ async function _validateNativeWorkflow(wf, cache, prefix, service) {
     return results;
 }
 async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache, service) {
+    if (!cache) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_no_tool_state",
+            errors: ["tool state validation disabled"],
+        };
+    }
     const resolved = await resolveTool(cache, toolId, toolVersion, service);
     if (isResolveError(resolved)) {
         const reason = describeResolveError(resolved);
@@ -225,11 +248,25 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache,
     const bundle = {
         parameters: resolved.tool.inputs,
     };
-    const connections = {};
-    for (const [key, val] of Object.entries(step.input_connections)) {
-        connections[key] = val;
-    }
-    return _validateNativeState(bundle, step.tool_state, connections, stepLabel, toolId, toolVersion);
+    return _validateNativeState(bundle, step.tool_state, step.input_connections, stepLabel, toolId, toolVersion, step.when);
+}
+function _validateEmbeddedNativeStep(step, stepLabel, repr, cache) {
+    if (!cache)
+        return _stateValidationDisabled(stepLabel, repr);
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateNativeState(tool.bundle, step.tool_state, step.input_connections, stepLabel, tool.toolId, tool.toolVersion, step.when);
+}
+function _stateValidationDisabled(stepLabel, repr) {
+    const { toolId, toolVersion } = embeddedToolIdentity(repr);
+    return {
+        step: stepLabel,
+        tool_id: toolId,
+        version: toolVersion,
+        status: "skip_no_tool_state",
+        errors: ["tool state validation disabled"],
+    };
 }
 /**
  * Validate a native-encoded tool_state block against the `workflow_step_native`
@@ -238,7 +275,29 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache,
  * encoding (double-encoded scalars, inline ConnectedValue/RuntimeValue markers)
  * is identical regardless of workflow format, so the same model validates both.
  */
-function _validateNativeState(bundle, toolState, connections, stepLabel, toolId, toolVersion) {
+/**
+ * Connection keys that feed the step itself rather than the tool: Galaxy wires
+ * a conditional step's skip-if expression through `input_connections`, under
+ * the literal key `when` in native form and under whatever names the format2
+ * `when:` expression references. Neither names a tool parameter, so neither is
+ * matched by the parameter walk.
+ */
+function stepLevelConnectionKeys(whenExpression) {
+    const keys = new Set(["when"]);
+    if (typeof whenExpression === "string") {
+        for (const m of whenExpression.matchAll(/inputs\.([A-Za-z_]\w*)/g))
+            keys.add(m[1]);
+        for (const m of whenExpression.matchAll(/inputs\[['"]([^'"]+)['"]\]/g))
+            keys.add(m[1]);
+    }
+    return keys;
+}
+/** Connection keys that matched no tool parameter and are not step-level inputs. */
+function unmatchedConnectionKeys(remaining, whenExpression) {
+    const stepLevel = stepLevelConnectionKeys(whenExpression);
+    return Object.keys(remaining).filter((k) => !stepLevel.has(k));
+}
+function _validateNativeState(bundle, toolState, connections, stepLabel, toolId, toolVersion, whenExpression) {
     // Skip validation if replacement parameters (${...}) are present in typed fields
     const replacementScan = scanForReplacements(bundle.parameters, toolState);
     if (replacementScan === "yes") {
@@ -252,7 +311,19 @@ function _validateNativeState(bundle, toolState, connections, stepLabel, toolId,
     }
     // Deep copy state and inject connection markers
     const state = structuredClone(toolState);
-    injectConnectionsIntoState(bundle.parameters, state, connections);
+    const remaining = injectConnectionsIntoState(bundle.parameters, state, connections);
+    // A connection key that matches no parameter is a defect whichever state block
+    // the step carries; the `state` path reports it below and this one must agree.
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, whenExpression);
+    if (unmatchedKeys.length > 0) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+        };
+    }
     const fieldModel = createFieldModel(bundle, "workflow_step_native");
     if (!fieldModel) {
         return {
@@ -279,6 +350,10 @@ function _validateNativeState(bundle, toolState, connections, stepLabel, toolId,
     return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }
 // --- Format2 validation ---
+/**
+ * Validate (or, when `cache` is null, merely enumerate) the tool steps of a
+ * format2 workflow. See {@link validateNativeSteps} for the null-cache behavior.
+ */
 export async function validateFormat2Steps(data, cache, prefix = "", expansionOpts, service) {
     const expanded = await expandedFormat2(data, expansionOpts);
     return _validateFormat2Workflow(expanded, cache, prefix, service);
@@ -288,6 +363,10 @@ async function _validateFormat2Workflow(wf, cache, prefix, service) {
     for (let i = 0; i < wf.steps.length; i++) {
         const step = wf.steps[i];
         const stepLabel = prefix ? `${prefix}${i}` : String(i);
+        if (isGalaxyUserToolRun(step.run)) {
+            results.push(_validateEmbeddedFormat2Step(step, stepLabel, step.run, cache));
+            continue;
+        }
         // Recurse into inline subworkflows
         if (step.run && typeof step.run === "object") {
             const subResults = await _validateFormat2Workflow(step.run, cache, `${stepLabel}.`, service);
@@ -304,6 +383,15 @@ async function _validateFormat2Workflow(wf, cache, prefix, service) {
     return results;
 }
 async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache, service) {
+    if (!cache) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_no_tool_state",
+            errors: ["tool state validation disabled"],
+        };
+    }
     const resolved = await resolveTool(cache, toolId, toolVersion, service);
     if (isResolveError(resolved)) {
         const reason = describeResolveError(resolved);
@@ -318,19 +406,32 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache,
     const bundle = {
         parameters: resolved.tool.inputs,
     };
+    return _validateFormat2State(bundle, step, stepLabel, toolId, toolVersion);
+}
+function _validateEmbeddedFormat2Step(step, stepLabel, repr, cache) {
+    if (!cache)
+        return _stateValidationDisabled(stepLabel, repr);
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateFormat2State(tool.bundle, step, stepLabel, tool.toolId, tool.toolVersion);
+}
+function _validateFormat2State(bundle, step, stepLabel, toolId, toolVersion) {
     // A step carries either a schema-aware `state` block or a verbatim native
     // `tool_state` block (gxformat2's state-unaware conversion copies the latter).
     // State shape — not workflow format — picks the validator: tool_state validates
     // through the native path, the same one native-body steps use.
     if (isEmptyState(step.state) && !isEmptyState(step.tool_state)) {
-        return _validateNativeState(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion);
+        return _validateNativeState(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion, step.when);
     }
     // Only the schema-aware `state` block is validatable. Deep-copy and strip
     // ConnectedValue markers left by $link normalization — these are captured in
     // step.in and will be injected during linked validation.
     const state = structuredClone((step.state ?? {}));
     stripConnectedValues(bundle.parameters, state);
-    // Level 1: Validate base state against workflow_step
+    const connections = nativeConnectionsFromFormat2In(step.in);
+    // Level 1: validate the stored, unlinked editor state. All fields are
+    // optional in workflow_step, but present values must still be well typed.
     const baseModel = createFieldModel(bundle, "workflow_step");
     if (!baseModel) {
         return {
@@ -354,53 +455,44 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache,
             errors: formatIssues(baseResult.left),
         };
     }
-    // Build connections dict from step.in entries
-    const connections = {};
-    for (const stepInput of step.in) {
-        if (stepInput.id && stepInput.source) {
-            const src = stepInput.source;
-            connections[stepInput.id] = Array.isArray(src) ? src : [src];
-        }
+    // Level 2: validate effective state after connection injection. This pass is
+    // required even with no connections because it restores required fields.
+    const linkedState = structuredClone(state);
+    const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
+        linked: true,
+    });
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, step.when);
+    if (unmatchedKeys.length > 0) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+        };
     }
-    // Level 2: Validate with connections injected against workflow_step_linked
-    if (Object.keys(connections).length > 0) {
-        const linkedState = structuredClone(state);
-        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
-            linked: true,
-        });
-        const unmatchedKeys = Object.keys(remaining);
-        if (unmatchedKeys.length > 0) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "fail",
-                errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
-            };
-        }
-        const linkedModel = createFieldModel(bundle, "workflow_step_linked");
-        if (!linkedModel) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "skip_tool_not_found",
-                errors: ["unsupported parameter types"],
-            };
-        }
-        const linkedValidate = S.decodeUnknownEither(linkedModel, {
-            onExcessProperty: "ignore",
-        });
-        const linkedResult = linkedValidate(linkedState);
-        if (linkedResult._tag === "Left") {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "fail",
-                errors: formatIssues(linkedResult.left),
-            };
-        }
+    const linkedModel = createFieldModel(bundle, "workflow_step_linked");
+    if (!linkedModel) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: ["unsupported parameter types"],
+        };
+    }
+    const linkedValidate = S.decodeUnknownEither(linkedModel, {
+        onExcessProperty: "ignore",
+    });
+    const linkedResult = linkedValidate(linkedState);
+    if (linkedResult._tag === "Left") {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatIssues(linkedResult.left),
+        };
     }
     return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }

package/dist/commands/validate-workflow.js.map

@@ -1 +1 @@
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package/dist/programs/galaxy-tool-cache.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"galaxy-tool-cache.d.ts","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqBzC,wBAAgB,2BAA2B,IAAI,OAAO,CAErD"}
+{"version":3,"file":"galaxy-tool-cache.d.ts","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuBzC,wBAAgB,2BAA2B,IAAI,OAAO,CAErD"}

package/dist/programs/galaxy-tool-cache.js

@@ -1,4 +1,5 @@
 import { runAdd } from "../commands/add.js";
+import { runAddLocal } from "../commands/add-local.js";
 import { runList } from "../commands/list.js";
 import { runInfo } from "../commands/info.js";
 import { runClear } from "../commands/clear.js";
@@ -9,6 +10,7 @@ import { buildProgramFromSpec } from "../spec/build-program.js";
 import { galaxyToolCacheSpec } from "../meta/specs.js";
 const handlers = {
     add: runAdd,
+    addLocal: runAddLocal,
     list: runList,
     info: runInfo,
     clear: runClear,

package/dist/programs/galaxy-tool-cache.js.map

@@ -1 +1 @@
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+{"version":3,"file":"galaxy-tool-cache.js","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAC;AACvD,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAwB,MAAM,0BAA0B,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kBAAkB,CAAC;AAEvD,MAAM,QAAQ,GAAoB;IAChC,GAAG,EAAE,MAAM;IACX,QAAQ,EAAE,WAAW;IACrB,IAAI,EAAE,OAAO;IACb,IAAI,EAAE,OAAO;IACb,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,SAAS;IACjB,SAAS,EAAE,YAAY;IACvB,gBAAgB,EAAE,mBAAmB;CACtC,CAAC;AAEF,MAAM,UAAU,2BAA2B;IACzC,OAAO,oBAAoB,CAAC,mBAAmB,EAAE,QAAQ,CAAC,CAAC;AAC7D,CAAC"}

package/dist/spec/build-program.js

@@ -39,7 +39,9 @@ function validateSpec(spec, handlers) {
         if (!handlers[cmd.handler]) {
             throw new Error(`Missing handler "${cmd.handler}" for command "${cmd.name}"`);
         }
-        const seenOptions = new Set();
+        // A boolean may declare both `--foo` and `--no-foo`; they share one
+        // attribute name but are distinct flags, so track the two senses apart.
+        const seenOptions = new Map();
         const checkOptName = (flags) => {
             const optName = attributeNameFromFlags(flags);
             if (RESERVED_OPTION_NAMES.has(optName)) {
@@ -47,10 +49,16 @@ function validateSpec(spec, handlers) {
                     `--${optName} flag (it would silently trigger ${optName === "version" ? "the version" : "the help"} ` +
                     `action instead of binding). Rename it (e.g. --tool-version).`);
             }
-            if (seenOptions.has(optName)) {
+            const negated = isNegatedFlag(flags);
+            const senses = seenOptions.get(optName);
+            if (!senses) {
+                seenOptions.set(optName, new Set([negated]));
+                return;
+            }
+            if (senses.has(negated)) {
                 throw new Error(`Duplicate option "${optName}" on command "${cmd.name}"`);
             }
-            seenOptions.add(optName);
+            senses.add(negated);
         };
         for (const opt of cmd.options ?? [])
             checkOptName(opt.flags);
@@ -70,6 +78,11 @@ function validateSpec(spec, handlers) {
  * for duplicate detection here; commander itself owns the canonical
  * derivation at runtime.
  */
+/** True when the option's long flag is commander's `--no-` negation form. */
+function isNegatedFlag(flags) {
+    const long = flags.split(/[ ,|]+/).find((part) => part.startsWith("--"));
+    return long?.startsWith("--no-") ?? false;
+}
 function attributeNameFromFlags(flags) {
     const long = flags.split(/[ ,|]+/).find((part) => part.startsWith("--"));
     if (!long)

package/dist/spec/build-program.js.map

@@ -1 +1 @@
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+{"version":3,"file":"build-program.js","sourceRoot":"","sources":["../../src/spec/build-program.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMpC;;;;;GAKG;AACH,MAAM,qBAAqB,GAAG,IAAI,GAAG,CAAC,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC,CAAC;AAE3D,MAAM,UAAU,oBAAoB,CAAC,IAAiB,EAAE,QAAyB;IAC/E,YAAY,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;IAC7B,MAAM,OAAO,GAAG,IAAI,OAAO,EAAE,CAAC;IAC9B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC5E,MAAM,MAAM,GAAG,IAAI,CAAC,YAAY,IAAI,EAAE,CAAC;IACvC,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAChC,OAAO,CAAC,UAAU,CAAC,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;IAC9F,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;GAKG;AACH,SAAS,YAAY,CAAC,IAAiB,EAAE,QAAyB;IAChE,MAAM,MAAM,GAAG,IAAI,CAAC,YAAY,IAAI,EAAE,CAAC;IACvC,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAC;IACvC,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAChC,IAAI,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,MAAM,IAAI,KAAK,CAAC,sBAAsB,GAAG,CAAC,IAAI,cAAc,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC;QAC5E,CAAC;QACD,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC3B,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;YAC3B,MAAM,IAAI,KAAK,CAAC,oBAAoB,GAAG,CAAC,OAAO,kBAAkB,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC;QAChF,CAAC;QACD,oEAAoE;QACpE,wEAAwE;QACxE,MAAM,WAAW,GAAG,IAAI,GAAG,EAAwB,CAAC;QACpD,MAAM,YAAY,GAAG,CAAC,KAAa,EAAQ,EAAE;YAC3C,MAAM,OAAO,GAAG,sBAAsB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,qBAAqB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBACvC,MAAM,IAAI,KAAK,CACb,aAAa,OAAO,iBAAiB,GAAG,CAAC,IAAI,uCAAuC;oBAClF,KAAK,OAAO,oCAAoC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,GAAG;oBACrG,8DAA8D,CACjE,CAAC;YACJ,CAAC;YACD,MAAM,OAAO,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC;YACrC,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;YACxC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;gBAC7C,OAAO;YACT,CAAC;YACD,IAAI,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBACxB,MAAM,IAAI,KAAK,CAAC,qBAAqB,OAAO,iBAAiB,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC;YAC5E,CAAC;YACD,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QACtB,CAAC,CAAC;QACF,KAAK,MAAM,GAAG,IAAI,GAAG,CAAC,OAAO,IAAI,EAAE;YAAE,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAC7D,KAAK,MAAM,SAAS,IAAI,GAAG,CAAC,YAAY,IAAI,EAAE,EAAE,CAAC;YAC/C,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC;YAChC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,MAAM,IAAI,KAAK,CAAC,YAAY,GAAG,CAAC,IAAI,qCAAqC,SAAS,GAAG,CAAC,CAAC;YACzF,CAAC;YACD,KAAK,MAAM,GAAG,IAAI,KAAK;gBAAE,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QACnD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,6EAA6E;AAC7E,SAAS,aAAa,CAAC,KAAa;IAClC,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC;IACzE,OAAO,IAAI,EAAE,UAAU,CAAC,OAAO,CAAC,IAAI,KAAK,CAAC;AAC5C,CAAC;AAED,SAAS,sBAAsB,CAAC,KAAa;IAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC;IACzE,IAAI,CAAC,IAAI;QAAE,OAAO,KAAK,CAAC;IACxB,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;IAC/C,OAAO,QAAQ,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,EAAE,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;AAC3E,CAAC;AAED,SAAS,YAAY,CACnB,IAAiB,EACjB,MAAoC,EACpC,QAAyB;IAEzB,MAAM,GAAG,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;IACjE,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,IAAI,EAAE,EAAE,CAAC;QAClC,IAAI,GAAG,CAAC,WAAW,KAAK,SAAS;YAAE,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,WAAW,CAAC,CAAC;;YACrE,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IAC7B,CAAC;IACD,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,OAAO,IAAI,EAAE,EAAE,CAAC;QACrC,SAAS,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;IACtB,CAAC;IACD,KAAK,MAAM,SAAS,IAAI,IAAI,CAAC,YAAY,IAAI,EAAE,EAAE,CAAC;QAChD,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC;QAChC,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,CAAC,IAAI,qCAAqC,SAAS,GAAG,CAAC,CAAC;QAC1F,CAAC;QACD,KAAK,MAAM,GAAG,IAAI,KAAK;YAAE,SAAS,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;IAC/C,CAAC;IACD,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACvC,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,IAAI,KAAK,CAAC,oBAAoB,IAAI,CAAC,OAAO,kBAAkB,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC;IAClF,CAAC;IACD,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;IACpB,OAAO,GAAG,CAAC;AACb,CAAC;AAED,SAAS,SAAS,CAAC,GAAY,EAAE,GAAe;IAC9C,IAAI,GAAG,CAAC,OAAO,KAAK,SAAS,EAAE,CAAC;QAC9B,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,WAAW,EAAE,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC;IAC9D,CAAC;SAAM,CAAC;QACN,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,WAAW,CAAC,CAAC;IACzC,CAAC;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.10.1",
+  "version": "1.13.1",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -39,10 +39,11 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/connection-validation": "1.10.1",
-    "@galaxy-tool-util/core": "1.10.1",
-    "@galaxy-tool-util/schema": "1.10.1",
-    "@galaxy-tool-util/search": "1.10.1"
+    "@galaxy-tool-util/schema": "1.13.1",
+    "@galaxy-tool-util/core": "1.13.1",
+    "@galaxy-tool-util/search": "1.13.1",
+    "@galaxy-tool-util/tool-xml": "1.13.1",
+    "@galaxy-tool-util/connection-validation": "1.13.1"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",

package/spec/galaxy-tool-cache.json

@@ -28,6 +28,31 @@
         }
       ]
     },
+    {
+      "name": "add-local",
+      "description": "Parse a local tool file (XML or YAML) and cache it (source: local)",
+      "handler": "addLocal",
+      "args": [
+        {
+          "raw": "<tool_path>",
+          "description": "Path to a tool file (.xml or .yml)"
+        }
+      ],
+      "options": [
+        {
+          "flags": "--tool-id <id>",
+          "description": "Full toolshed tool_id for cache keying (required; the bare XML id is not a valid key)"
+        },
+        {
+          "flags": "--tool-version <ver>",
+          "description": "Tool version (overrides the parsed version)"
+        },
+        {
+          "flags": "--cache-dir <dir>",
+          "description": "Cache directory"
+        }
+      ]
+    },
     {
       "name": "list",
       "description": "List cached tools with their resolved versions",

package/spec/gxwf.json

@@ -312,11 +312,15 @@
         },
         {
           "flags": "--stateful",
-          "description": "Use cached tool definitions for schema-aware state re-encoding"
+          "description": "Force schema-aware state re-encoding even if the tool cache is empty"
+        },
+        {
+          "flags": "--no-stateful",
+          "description": "Skip schema-aware state re-encoding; copy tool_state through verbatim"
         },
         {
           "flags": "--cache-dir <dir>",
-          "description": "Tool cache directory (for --stateful)"
+          "description": "Tool cache directory (default: schema-aware re-encoding when it is populated)"
         }
       ],
       "optionGroups": ["strict"]
@@ -596,11 +600,15 @@
         },
         {
           "flags": "--stateful",
-          "description": "Use cached tool definitions for schema-aware state re-encoding"
+          "description": "Force schema-aware state re-encoding even if the tool cache is empty"
+        },
+        {
+          "flags": "--no-stateful",
+          "description": "Skip schema-aware state re-encoding; copy tool_state through verbatim"
         },
         {
           "flags": "--cache-dir <dir>",
-          "description": "Tool cache directory (for --stateful)"
+          "description": "Tool cache directory (default: schema-aware re-encoding when it is populated)"
         }
       ],
       "optionGroups": ["strict"]