@galaxy-tool-util/cli 1.10.0 → 1.12.0

package/dist/commands/add-local.d.ts

@@ -0,0 +1,15 @@
+export interface AddLocalOptions {
+    toolId?: string;
+    toolVersion?: string;
+    cacheDir?: string;
+}
+/**
+ * Cache a tool parsed from a local file — the local-ingest counterpart to `add`
+ * (which fetches from the ToolShed). Dispatches on extension like Galaxy's
+ * `get_tool_source` (`.yml` → YAML, else → XML; CWL unsupported). Mirrors
+ * Galaxy's `run_add_local`: a bare `<tool id>` is not a valid cache key, so
+ * `--tool-id` (the full toolshed tool_id) is required even when the file carries
+ * an id; the parsed id is surfaced only as a hint.
+ */
+export declare function runAddLocal(toolPath: string, opts: AddLocalOptions): Promise<void>;
+//# sourceMappingURL=add-local.d.ts.map

package/dist/commands/add-local.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-local.d.ts","sourceRoot":"","sources":["../../src/commands/add-local.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;GAOG;AACH,wBAAsB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAkCxF"}

package/dist/commands/add-local.js

@@ -0,0 +1,44 @@
+import { makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
+import { loadToolFile } from "@galaxy-tool-util/tool-xml";
+/**
+ * Cache a tool parsed from a local file — the local-ingest counterpart to `add`
+ * (which fetches from the ToolShed). Dispatches on extension like Galaxy's
+ * `get_tool_source` (`.yml` → YAML, else → XML; CWL unsupported). Mirrors
+ * Galaxy's `run_add_local`: a bare `<tool id>` is not a valid cache key, so
+ * `--tool-id` (the full toolshed tool_id) is required even when the file carries
+ * an id; the parsed id is surfaced only as a hint.
+ */
+export async function runAddLocal(toolPath, opts) {
+    let parsed;
+    try {
+        parsed = loadToolFile(toolPath);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        console.error(`Failed to parse ${toolPath}: ${msg}`);
+        process.exitCode = 1;
+        return;
+    }
+    const toolId = opts.toolId;
+    if (toolId == null) {
+        if (parsed.id && parsed.version) {
+            console.log(`Parsed tool: ${parsed.id} v${parsed.version}`);
+            console.log("Use --tool-id to specify the full toolshed tool_id for proper cache keying.");
+            process.exitCode = 1;
+            return;
+        }
+        console.error("Cannot determine tool_id from tool file. Use --tool-id.");
+        process.exitCode = 1;
+        return;
+    }
+    const version = opts.toolVersion || parsed.version;
+    if (version == null) {
+        console.error("Cannot determine version. Use --tool-version.");
+        process.exitCode = 1;
+        return;
+    }
+    const service = makeNodeToolInfoService({ cacheDir: opts.cacheDir });
+    await service.addTool(toolId, version, parsed, "local", toolPath);
+    console.log(`Cached ${toolId} ${version} from ${toolPath}`);
+}
+//# sourceMappingURL=add-local.js.map

package/dist/commands/add-local.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-local.js","sourceRoot":"","sources":["../../src/commands/add-local.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AACtE,OAAO,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAC;AAQ1D;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,QAAgB,EAAE,IAAqB;IACvE,IAAI,MAAM,CAAC;IACX,IAAI,CAAC;QACH,MAAM,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAC;IAClC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO,CAAC,KAAK,CAAC,mBAAmB,QAAQ,KAAK,GAAG,EAAE,CAAC,CAAC;QACrD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC;IAC3B,IAAI,MAAM,IAAI,IAAI,EAAE,CAAC;QACnB,IAAI,MAAM,CAAC,EAAE,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAChC,OAAO,CAAC,GAAG,CAAC,gBAAgB,MAAM,CAAC,EAAE,KAAK,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC;YAC5D,OAAO,CAAC,GAAG,CAAC,6EAA6E,CAAC,CAAC;YAC3F,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;YACrB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;QACzE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,CAAC,WAAW,IAAI,MAAM,CAAC,OAAO,CAAC;IACnD,IAAI,OAAO,IAAI,IAAI,EAAE,CAAC;QACpB,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;QAC/D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,uBAAuB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACrE,MAAM,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,UAAU,MAAM,IAAI,OAAO,SAAS,QAAQ,EAAE,CAAC,CAAC;AAC9D,CAAC"}

package/dist/commands/lint-tree.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAcA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,eAAgB,SAAQ,aAAa,EAAE,mBAAmB;IACzE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAUD,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAyEnF"}
+{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAcA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,eAAgB,SAAQ,aAAa,EAAE,mBAAmB;IACzE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAUD,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0EnF"}

package/dist/commands/lint-tree.js

@@ -73,7 +73,8 @@ export async function runLintTree(dir, opts) {
     }
     const s = report.summary;
     const total = report.workflows.length;
-    console.log(`\nSummary: ${total} workflows | ${s.lint_errors} errors, ${s.lint_warnings} warnings, ${s.state_fail} state failures`);
+    const loadErrorSuffix = s.errors > 0 ? `, ${s.errors} load errors` : "";
+    console.log(`\nSummary: ${total} workflows | ${s.lint_errors} errors, ${s.lint_warnings} warnings, ${s.state_fail} state failures${loadErrorSuffix}`);
     process.exitCode = computeLintExitCode(report);
 }
 function buildReport(treeResult) {

package/dist/commands/lint-tree.js.map

@@ -1 +1 @@
-{"version":3,"file":"lint-tree.js","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAKhE,OAAO,EACL,uBAAuB,EACvB,mBAAmB,IAAI,yBAAyB,GACjD,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,kBAAkB,EAAmB,MAAM,WAAW,CAAC;AAChE,OAAO,EAAE,WAAW,EAAmB,MAAM,WAAW,CAAC;AACzD,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAA4B,MAAM,oBAAoB,CAAC;AAUlG,0EAA0E;AAC1E,SAAS,oBAAoB,CAAC,YAAoB,EAAE,EAAc;IAChE,MAAM,WAAW,GAAG,EAAE,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,aAAa,GAAG,EAAE,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,WAAW,GAAG,EAAE,CAAC,eAAe,IAAI,EAAE,CAAC;IAC7C,OAAO,uBAAuB,CAAC,YAAY,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;AACxF,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,GAAW,EAAE,IAAqB;IAClE,qCAAqC;IACrC,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACvD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/C,OAAO,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;gBACnF,KAAK,GAAG,SAAS,CAAC;YACpB,CAAC;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,UAAU,GAAG,MAAM,WAAW,CAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACjF,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,EAAE,GAAG,MAAM,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE;YAC3D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;YACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;YAC7C,KAAK;YACL,MAAM;SACP,CAAC,CAAC;QACH,OAAO,oBAAoB,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,WAAW,CAAC,UAAU,CAAC,CAAC;IAEvC,MAAM,iBAAiB,CAAC,iBAAiB,EAAE,MAAM,EAAE,EAAE,cAAc,EAAE,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IAC5F,MAAM,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAE5D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC/C,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QAClC,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC;YACnD,SAAS;QACX,CAAC;QACD,IAAI,EAAE,CAAC,cAAc,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC,cAAc,GAAG,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QAED,MAAM,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,CAAC;QAExE,IAAI,EAAE,CAAC,WAAW,GAAG,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACzC,OAAO,CAAC,KAAK,CACX,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,WAAW,YAAY,EAAE,CAAC,aAAa,cAAc,UAAU,iBAAiB,CACrG,CAAC;YACF,+DAA+D;YAC/D,2DAA2D;QAC7D,CAAC;aAAM,IAAI,EAAE,CAAC,aAAa,GAAG,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,aAAa,WAAW,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IACtC,OAAO,CAAC,GAAG,CACT,cAAc,KAAK,gBAAgB,CAAC,CAAC,WAAW,YAAY,CAAC,CAAC,aAAa,cAAc,CAAC,CAAC,UAAU,iBAAiB,CACvH,CAAC;IACF,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,WAAW,CAAC,UAA0C;IAC7D,MAAM,SAAS,GAAyB,EAAE,CAAC;IAE3C,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,SAAS,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;YAC3F,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,SAAS,CAAC,IAAI,CACZ,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;gBACrD,cAAc,EAAG,CAAC,CAAC,UAAgC,IAAI,IAAI;aAC5D,CAAC,CACH,CAAC;YACF,SAAS;QACX,CAAC;QACD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,MAAO,CAAC,CAAC;IAC5B,CAAC;IAED,OAAO,yBAAyB,CAAC,UAAU,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;AAC/D,CAAC;AAED,SAAS,mBAAmB,CAAC,MAA4B;IACvD,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,IAAI,CAAC,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACpE,IAAI,CAAC,CAAC,aAAa,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IAClC,OAAO,CAAC,CAAC;AACX,CAAC"}
+{"version":3,"file":"lint-tree.js","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAKhE,OAAO,EACL,uBAAuB,EACvB,mBAAmB,IAAI,yBAAyB,GACjD,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,kBAAkB,EAAmB,MAAM,WAAW,CAAC;AAChE,OAAO,EAAE,WAAW,EAAmB,MAAM,WAAW,CAAC;AACzD,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAA4B,MAAM,oBAAoB,CAAC;AAUlG,0EAA0E;AAC1E,SAAS,oBAAoB,CAAC,YAAoB,EAAE,EAAc;IAChE,MAAM,WAAW,GAAG,EAAE,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,aAAa,GAAG,EAAE,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,WAAW,GAAG,EAAE,CAAC,eAAe,IAAI,EAAE,CAAC;IAC7C,OAAO,uBAAuB,CAAC,YAAY,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;AACxF,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,GAAW,EAAE,IAAqB;IAClE,qCAAqC;IACrC,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACvD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/C,OAAO,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;gBACnF,KAAK,GAAG,SAAS,CAAC;YACpB,CAAC;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,UAAU,GAAG,MAAM,WAAW,CAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACjF,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,EAAE,GAAG,MAAM,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE;YAC3D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;YACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;YAC7C,KAAK;YACL,MAAM;SACP,CAAC,CAAC;QACH,OAAO,oBAAoB,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,WAAW,CAAC,UAAU,CAAC,CAAC;IAEvC,MAAM,iBAAiB,CAAC,iBAAiB,EAAE,MAAM,EAAE,EAAE,cAAc,EAAE,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IAC5F,MAAM,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAE5D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC/C,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QAClC,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC;YACnD,SAAS;QACX,CAAC;QACD,IAAI,EAAE,CAAC,cAAc,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC,cAAc,GAAG,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QAED,MAAM,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,CAAC;QAExE,IAAI,EAAE,CAAC,WAAW,GAAG,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACzC,OAAO,CAAC,KAAK,CACX,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,WAAW,YAAY,EAAE,CAAC,aAAa,cAAc,UAAU,iBAAiB,CACrG,CAAC;YACF,+DAA+D;YAC/D,2DAA2D;QAC7D,CAAC;aAAM,IAAI,EAAE,CAAC,aAAa,GAAG,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,aAAa,WAAW,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IACtC,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC;IACxE,OAAO,CAAC,GAAG,CACT,cAAc,KAAK,gBAAgB,CAAC,CAAC,WAAW,YAAY,CAAC,CAAC,aAAa,cAAc,CAAC,CAAC,UAAU,kBAAkB,eAAe,EAAE,CACzI,CAAC;IACF,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,WAAW,CAAC,UAA0C;IAC7D,MAAM,SAAS,GAAyB,EAAE,CAAC;IAE3C,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,SAAS,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;YAC3F,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,SAAS,CAAC,IAAI,CACZ,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;gBACrD,cAAc,EAAG,CAAC,CAAC,UAAgC,IAAI,IAAI;aAC5D,CAAC,CACH,CAAC;YACF,SAAS;QACX,CAAC;QACD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,MAAO,CAAC,CAAC;IAC5B,CAAC;IAED,OAAO,yBAAyB,CAAC,UAAU,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;AAC/D,CAAC;AAED,SAAS,mBAAmB,CAAC,MAA4B;IACvD,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,IAAI,CAAC,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACpE,IAAI,CAAC,CAAC,aAAa,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IAClC,OAAO,CAAC,CAAC;AACX,CAAC"}

package/dist/commands/tool-search.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"tool-search.d.ts","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAGlE,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,UAAU,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAQD,wBAAsB,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA2DzF"}
+{"version":3,"file":"tool-search.d.ts","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAGlE,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,UAAU,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAQD,wBAAsB,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA+CzF"}

package/dist/commands/tool-search.js

@@ -1,6 +1,6 @@
 import { DEFAULT_TOOLSHED_URL } from "@galaxy-tool-util/core";
 import { makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
-import { ToolFetchError, iterateToolSearchPages, normalizeHit } from "@galaxy-tool-util/search";
+import { ToolFetchError, ToolSearchService } from "@galaxy-tool-util/search";
 function toInt(value, fallback) {
     if (value === undefined)
         return fallback;
@@ -11,26 +11,27 @@ export async function runToolSearch(query, opts) {
     const pageSize = toInt(opts.pageSize, 20);
     const maxResults = toInt(opts.maxResults, 50);
     const page = toInt(opts.page, 1);
-    const owner = opts.owner?.toLowerCase();
-    const matchName = opts.matchName === true;
-    const queryTokens = queryNameTokens(query);
     const source = { type: "toolshed", url: DEFAULT_TOOLSHED_URL };
-    const hits = [];
+    const onDiagnostic = (message) => console.error(message);
+    const info = makeNodeToolInfoService({
+        cacheDir: opts.cacheDir,
+        onDiagnostic,
+    });
+    const search = new ToolSearchService({
+        sources: [source],
+        info,
+        onDiagnostic,
+    });
+    let hits;
     try {
-        for await (const pageResults of iterateToolSearchPages(source.url, query, { pageSize, page })) {
-            for (const raw of pageResults.hits) {
-                const hit = normalizeHit(raw, source);
-                if (owner !== undefined && hit.repoOwnerUsername.toLowerCase() !== owner)
-                    continue;
-                if (matchName && !nameMatchesQuery(hit.toolName, queryTokens))
-                    continue;
-                hits.push(hit);
-                if (hits.length >= maxResults)
-                    break;
-            }
-            if (hits.length >= maxResults)
-                break;
-        }
+        hits = await search.searchTools(query, {
+            page,
+            pageSize,
+            maxResults,
+            owner: opts.owner,
+            matchName: opts.matchName,
+            enrich: opts.enrich,
+        });
     }
     catch (err) {
         if (err instanceof ToolFetchError) {
@@ -40,21 +41,6 @@ export async function runToolSearch(query, opts) {
         }
         throw err;
     }
-    hits.sort((a, b) => b.score - a.score);
-    if (opts.enrich && hits.length > 0) {
-        const info = makeNodeToolInfoService({ cacheDir: opts.cacheDir });
-        await Promise.all(hits.map(async (hit) => {
-            try {
-                const parsed = await info.getToolInfo(hit.trsToolId, hit.version ?? null);
-                if (parsed !== null)
-                    hit.parsedTool = parsed;
-            }
-            catch (err) {
-                const msg = err instanceof Error ? err.message : String(err);
-                console.error(`Enrichment failed for ${hit.trsToolId}: ${msg}`);
-            }
-        }));
-    }
     if (opts.json) {
         const envelope = { query, hits };
         console.log(JSON.stringify(envelope, null, 2));
@@ -89,19 +75,4 @@ function truncate(s, max) {
     const flat = s.replace(/\s+/g, " ").trim();
     return flat.length > max ? `${flat.slice(0, max - 1)}…` : flat;
 }
-function tokenize(s) {
-    return s
-        .toLowerCase()
-        .split(/[^a-z0-9+]+/)
-        .filter((t) => t.length > 0);
-}
-function queryNameTokens(query) {
-    return tokenize(query);
-}
-function nameMatchesQuery(name, queryTokens) {
-    if (queryTokens.length === 0)
-        return true;
-    const nameTokens = new Set(tokenize(name));
-    return queryTokens.some((t) => nameTokens.has(t));
-}
 //# sourceMappingURL=tool-search.js.map

package/dist/commands/tool-search.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tool-search.js","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAC9D,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAEtE,OAAO,EAAE,cAAc,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAkB7E,SAAS,KAAK,CAAC,KAAkC,EAAE,QAAgB;IACjE,IAAI,KAAK,KAAK,SAAS;QAAE,OAAO,QAAQ,CAAC;IACzC,MAAM,CAAC,GAAG,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;IAClE,OAAO,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;AACpD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,KAAa,EAAE,IAAuB;IACxE,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;IAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;IAC9C,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACjC,MAAM,MAAM,GAAe,EAAE,IAAI,EAAE,UAAU,EAAE,GAAG,EAAE,oBAAoB,EAAE,CAAC;IAC3E,MAAM,YAAY,GAAG,CAAC,OAAe,EAAQ,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACvE,MAAM,IAAI,GAAG,uBAAuB,CAAC;QACnC,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,YAAY;KACb,CAAC,CAAC;IACH,MAAM,MAAM,GAAG,IAAI,iBAAiB,CAAC;QACnC,OAAO,EAAE,CAAC,MAAM,CAAC;QACjB,IAAI;QACJ,YAAY;KACb,CAAC,CAAC;IAEH,IAAI,IAAyB,CAAC;IAC9B,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE;YACrC,IAAI;YACJ,QAAQ;YACR,UAAU;YACV,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,SAAS,EAAE,IAAI,CAAC,SAAS;YACzB,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,IAAI,GAAG,YAAY,cAAc,EAAE,CAAC;YAClC,OAAO,CAAC,KAAK,CAAC,4BAA4B,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;YACzD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;YACrB,OAAO;QACT,CAAC;QACD,MAAM,GAAG,CAAC;IACZ,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,MAAM,QAAQ,GAAyB,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;QACvD,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IACjD,CAAC;SAAM,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,OAAO,CAAC,KAAK,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAC;IAC/C,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC;IACjC,CAAC;IAED,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;IACvB,CAAC;AACH,CAAC;AAED,SAAS,WAAW,CAAC,IAAyB;IAC5C,MAAM,MAAM,GAAG,CAAC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,CAAC,CAAC;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;QAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAClB,GAAG,CAAC,CAAC,iBAAiB,IAAI,CAAC,CAAC,QAAQ,EAAE;QACtC,CAAC,CAAC,MAAM;QACR,CAAC,CAAC,QAAQ;QACV,QAAQ,CAAC,CAAC,CAAC,eAAe,IAAI,EAAE,EAAE,EAAE,CAAC;KACtC,CAAC,CAAC;IACH,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IAC7F,MAAM,GAAG,GAAG,CAAC,KAAe,EAAU,EAAE,CACtC,KAAK;SACF,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;SAClC,IAAI,CAAC,IAAI,CAAC;SACV,OAAO,EAAE,CAAC;IACf,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC3F,CAAC;AAED,SAAS,QAAQ,CAAC,CAAS,EAAE,GAAW;IACtC,MAAM,IAAI,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;IAC3C,OAAO,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;AACjE,CAAC"}

package/dist/commands/tree.d.ts

@@ -12,6 +12,12 @@ export interface WorkflowInfo {
     path: string;
     relativePath: string;
     format: WorkflowFormat;
+    /**
+     * Set when a file with an unambiguous workflow extension (.ga, .gxwf.yml,
+     * .gxwf.yaml) failed to parse during discovery. Such files are still
+     * reported (as an error outcome) rather than silently dropped.
+     */
+    loadError?: string;
 }
 export interface WorkflowOutcome<T> {
     info: WorkflowInfo;
@@ -33,6 +39,12 @@ export interface TreeSummary {
 }
 /** Call from processOne to skip a workflow with a reason. */
 export declare function skipWorkflow(reason: string): never;
+/**
+ * Collapse a multi-line message to its first line. Tree outcome errors land in
+ * the per-workflow console listing and in `|`-delimited Markdown report table
+ * cells, both of which a raw multi-line YAML parse error would wreck.
+ */
+export declare function firstLine(msg: string): string;
 /** Discover workflow files recursively under root. */
 export declare function discoverWorkflows(root: string, includeFormat2?: boolean): Promise<WorkflowInfo[]>;
 /** Load and parse a discovered workflow file. Returns null on failure. */

package/dist/commands/tree.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"tree.d.ts","sourceRoot":"","sources":["../../src/commands/tree.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAO/D,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,cAAc,CAAC;IACvB;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,eAAe,CAAC,CAAC;IAChC,IAAI,EAAE,YAAY,CAAC;IACnB,MAAM,CAAC,EAAE,CAAC,CAAC;IACX,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,UAAU,CAAC,CAAC;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC;CAChC;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;CACjB;AAKD,6DAA6D;AAC7D,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,KAAK,CAElD;AAqBD;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAG7C;AAqCD,sDAAsD;AACtD,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,MAAM,EACZ,cAAc,UAAO,GACpB,OAAO,CAAC,YAAY,EAAE,CAAC,CAKzB;AAiED,0EAA0E;AAC1E,wBAAsB,gBAAgB,CACpC,IAAI,EAAE,YAAY,GACjB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,CAOzC;AAID,MAAM,MAAM,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;AAElG,mEAAmE;AACnE,wBAAsB,WAAW,CAAC,CAAC,EACjC,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC,EACzB,cAAc,UAAO,GACpB,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CA4BxB;AAED,kDAAkD;AAClD,wBAAgB,iBAAiB,CAAC,CAAC,EACjC,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,EAC9B,MAAM,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,KAAK,OAAO,GAC9B,WAAW,CAiBb"}

package/dist/commands/tree.js

@@ -28,20 +28,40 @@ function classifyFile(filename) {
         return "format2";
     return null;
 }
+/**
+ * Collapse a multi-line message to its first line. Tree outcome errors land in
+ * the per-workflow console listing and in `|`-delimited Markdown report table
+ * cells, both of which a raw multi-line YAML parse error would wreck.
+ */
+export function firstLine(msg) {
+    const idx = msg.indexOf("\n");
+    return idx === -1 ? msg : msg.slice(0, idx);
+}
+/**
+ * True for extensions that unambiguously denote a Galaxy workflow (.ga,
+ * .gxwf.yml, .gxwf.yaml). A parse failure on one of these is a real error to
+ * surface; a parse failure on a plain .yml/.json could be any unrelated file
+ * and is skipped silently.
+ */
+function isDefiniteWorkflowExtension(filename) {
+    if (FORMAT2_SUFFIXES.some((suffix) => filename.endsWith(suffix)))
+        return true;
+    return NATIVE_EXTENSIONS.has(extname(filename));
+}
 function isWorkflowContent(data, format) {
     if (format === "native") {
         return data.a_galaxy_workflow === "true";
     }
     return data.class === "GalaxyWorkflow";
 }
+/** Parse raw workflow content; throws on malformed JSON/YAML. */
+function parseFileContentOrThrow(raw, format) {
+    const parsed = format === "native" ? JSON.parse(raw) : YAML.parse(raw);
+    return typeof parsed === "object" && parsed !== null ? parsed : null;
+}
 function parseFileContent(raw, format) {
     try {
-        if (format === "native") {
-            const parsed = JSON.parse(raw);
-            return typeof parsed === "object" && parsed !== null ? parsed : null;
-        }
-        const parsed = YAML.parse(raw);
-        return typeof parsed === "object" && parsed !== null ? parsed : null;
+        return parseFileContentOrThrow(raw, format);
     }
     catch {
         return null;
@@ -84,7 +104,23 @@ async function _walkDir(dir, root, includeFormat2, out) {
         catch {
             continue;
         }
-        const data = parseFileContent(raw, format);
+        let data;
+        try {
+            data = parseFileContentOrThrow(raw, format);
+        }
+        catch (e) {
+            // A malformed file with an unambiguous workflow extension is a real
+            // error to report; a malformed plain .yml/.json is some other file.
+            if (isDefiniteWorkflowExtension(entry.name)) {
+                out.push({
+                    path: filePath,
+                    relativePath: relative(root, filePath),
+                    format,
+                    loadError: e instanceof Error ? e.message : String(e),
+                });
+            }
+            continue;
+        }
         if (!data || !isWorkflowContent(data, format))
             continue;
         out.push({
@@ -110,6 +146,10 @@ export async function collectTree(root, processOne, includeFormat2 = true) {
     const workflows = await discoverWorkflows(root, includeFormat2);
     const outcomes = [];
     for (const info of workflows) {
+        if (info.loadError) {
+            outcomes.push({ info, error: firstLine(info.loadError) });
+            continue;
+        }
         const data = await loadWorkflowSafe(info);
         if (!data) {
             outcomes.push({ info, error: "Failed to load workflow" });
@@ -124,7 +164,7 @@ export async function collectTree(root, processOne, includeFormat2 = true) {
                 outcomes.push({ info, skipped: true, skipReason: e.message });
             }
             else {
-                outcomes.push({ info, error: e instanceof Error ? e.message : String(e) });
+                outcomes.push({ info, error: firstLine(e instanceof Error ? e.message : String(e)) });
             }
         }
     }

package/dist/commands/tree.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"validate-tree.d.ts","sourceRoot":"","sources":["../../src/commands/validate-tree.ts"],"names":[],"mappings":"AAiBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,mBAAoB,SAAQ,aAAa,EAAE,mBAAmB;IAC7E,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,wBAAsB,eAAe,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAgI3F"}

package/dist/commands/validate-tree.js

@@ -26,8 +26,12 @@ export async function runValidateTree(dir, opts) {
     let validateFormat2StepsJsonSchema;
     if (mode === "json-schema") {
         const mod = await import("./validate-workflow-json-schema.js");
-        validateNativeStepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
-        validateFormat2StepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
+        validateNativeStepsJsonSchema = (data, cache, prefix, expansionOpts) => cache
+            ? mod.validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts)
+            : Promise.resolve([]);
+        validateFormat2StepsJsonSchema = (data, cache, prefix, expansionOpts) => cache
+            ? mod.validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts)
+            : Promise.resolve([]);
     }
     const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
@@ -48,7 +52,7 @@ export async function runValidateTree(dir, opts) {
         const expansionOpts = {
             resolver: createDefaultResolver({ workflowDirectory: dirname(info.path) }),
         };
-        let stepResults = [];
+        let stepResults;
         if (cache && opts.toolState !== false) {
             const validateNative = validateNativeStepsJsonSchema ?? validateNativeSteps;
             const validateF2 = validateFormat2StepsJsonSchema ?? validateFormat2Steps;
@@ -57,8 +61,21 @@ export async function runValidateTree(dir, opts) {
                     ? await validateNative(data, cache, "", expansionOpts)
                     : await validateF2(data, cache, "", expansionOpts);
         }
-        // --strict-state: promote skips to failures
-        if (strict.strictState && stepResults.some((s) => s.status !== "ok" && s.status !== "fail")) {
+        else {
+            // Tool-state validation disabled (or no cache): still enumerate tool
+            // steps so the step count is reported, marking each as skipped. No
+            // resolver is passed — enumeration must stay offline, so subworkflow
+            // expansion is inline-only rather than fetching external references.
+            stepResults =
+                format === "native"
+                    ? await validateNativeSteps(data, null)
+                    : await validateFormat2Steps(data, null);
+        }
+        // --strict-state: promote skips to failures. `skip_no_tool_state` is
+        // exempt — it means the user turned tool-state validation off, not that a
+        // step could not be checked, and `gxwf validate` treats it the same way.
+        if (strict.strictState &&
+            stepResults.some((s) => s.status !== "ok" && s.status !== "fail" && s.status !== "skip_no_tool_state")) {
             throw new Error("Strict state: skipped steps not allowed");
         }
         return buildWorkflowValidationResult(info.relativePath, stepResults);
@@ -95,7 +112,8 @@ export async function runValidateTree(dir, opts) {
     }
     const s = report.summary;
     const total = report.workflows.length;
-    console.log(`\nSummary: ${total} workflows | ${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP`);
+    const errorSuffix = s.error > 0 ? `, ${s.error} ERROR` : "";
+    console.log(`\nSummary: ${total} workflows | ${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP${errorSuffix}`);
     process.exitCode = computeValidateExitCode(report);
 }
 function buildReport(treeResult) {

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

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

@@ -1 +1 @@
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+{"version":3,"file":"validate-workflow-json-schema.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow-json-schema.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAgBL,KAAK,gBAAgB,EACtB,MAAM,0BAA0B,CAAC;AAWlC,OAAO,KAAK,EACV,uBAAuB,EACvB,cAAc,EACd,oBAAoB,EACrB,MAAM,wBAAwB,CAAC;AAwJhC;;;;GAIG;AACH,wBAAgB,+BAA+B,CAC7C,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,GACrB,MAAM,EAAE,CAOV;AAID,wBAAsB,6BAA6B,CACjD,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,uBAAuB,EAC7B,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,IAAI,CAAC,CAsGf;AAID,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AAiJD,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC"}

package/dist/commands/validate-workflow-json-schema.js

@@ -8,7 +8,7 @@
  * Mirrors Galaxy's validation_json_schema.py.
  */
 import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
-import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, scanForReplacements, withClass, } from "@galaxy-tool-util/schema";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, scanForReplacements, withClass, } from "@galaxy-tool-util/schema";
 import * as JSONSchema from "effect/JSONSchema";
 import Ajv2020 from "ajv/dist/2020.js";
 import { readFileSync, existsSync } from "node:fs";
@@ -368,8 +368,17 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     if (isEmptyState(step.state) && !isEmptyState(step.tool_state)) {
         return _validateNativeStateJsonSchema(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion, toolSchemaDir);
     }
-    const state = (step.state ?? {});
-    // Level 1: base validation against workflow_step
+    const state = structuredClone((step.state ?? {}));
+    stripConnectedValues(bundle.parameters, state);
+    // Build connections dict from step.in
+    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 1: validate the stored, unlinked editor state.
     const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
     if (!baseValidate) {
         return {
@@ -390,43 +399,41 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
             errors: formatAjvErrors(baseValidate),
         };
     }
-    // Build connections dict from step.in
-    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. Always run
+    // this pass so missing, unconnected required values are rejected.
+    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}"`),
+        };
     }
-    // Level 2: linked validation with connections injected
-    if (Object.keys(connections).length > 0) {
-        const linkedState = structuredClone(state);
-        // Unmatched connection keys (e.g. the synthetic `when` gate on conditional
-        // steps) are discarded, not failed — mirrors Python's
-        // validate_workflow_json_schema, which injects connections and ignores the
-        // returned unmatched paths. (The Pydantic path raises on unmatched; the
-        // JSON Schema path is intentionally lenient.)
-        injectConnectionsIntoState(bundle.parameters, linkedState, connections, { linked: true });
-        const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
-        if (!linkedValidate) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "skip_tool_not_found",
-                errors: ["unsupported parameter types"],
-            };
-        }
-        const linkedValid = linkedValidate(linkedState);
-        if (!linkedValid) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "fail",
-                errors: formatAjvErrors(linkedValidate),
-            };
-        }
+    const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
+    if (!linkedValidate) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: ["unsupported parameter types"],
+        };
+    }
+    const linkedValid = linkedValidate(linkedState);
+    if (!linkedValid) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatAjvErrors(linkedValidate),
+        };
     }
     return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }

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

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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

@@ -1 +1 @@
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package/dist/commands/validate-workflow.js

@@ -187,6 +187,12 @@ 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);
@@ -211,6 +217,15 @@ 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 +240,7 @@ 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);
 }
 /**
  * Validate a native-encoded tool_state block against the `workflow_step_native`
@@ -279,6 +290,10 @@ 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);
@@ -304,6 +319,15 @@ 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);
@@ -330,7 +354,9 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache,
     // 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 +380,44 @@ 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 = 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 "${k}"`),
+        };
     }
-    // Level 2: Validate with connections injected against workflow_step_linked
-    if (Object.keys(connections).length > 0) {
-        const linkedState = structuredClone(state);
-        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
-            linked: true,
-        });
-        const unmatchedKeys = Object.keys(remaining);
-        if (unmatchedKeys.length > 0) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "fail",
-                errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${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 @@
-{"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,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,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"}
+{"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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.10.0",
+  "version": "1.12.0",
   "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": "1.10.0",
-    "@galaxy-tool-util/core": "1.10.0",
-    "@galaxy-tool-util/schema": "1.10.0",
-    "@galaxy-tool-util/search": "1.10.0"
+    "@galaxy-tool-util/schema": "1.12.0",
+    "@galaxy-tool-util/connection-validation": "1.12.0",
+    "@galaxy-tool-util/core": "1.12.0",
+    "@galaxy-tool-util/search": "1.12.0",
+    "@galaxy-tool-util/tool-xml": "1.12.0"
   },
   "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",