@galaxy-tool-util/cli 1.6.0 → 1.7.1

package/dist/commands/add.d.ts

@@ -1,5 +1,5 @@
 export interface AddOptions {
-    version?: string;
+    toolVersion?: string;
     cacheDir?: string;
     galaxyUrl?: string;
 }

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

@@ -1 +1 @@
-{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,UAAU;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAa5E"}
+{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,UAAU;IACzB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAa5E"}

package/dist/commands/add.js

@@ -4,7 +4,7 @@ export async function runAdd(toolId, opts) {
         cacheDir: opts.cacheDir,
         galaxyUrl: opts.galaxyUrl,
     });
-    const result = await service.getToolInfo(toolId, opts.version);
+    const result = await service.getToolInfo(toolId, opts.toolVersion);
     if (result === null) {
         console.error(`Failed to fetch tool: ${toolId}`);
         process.exitCode = 1;

package/dist/commands/add.js.map

@@ -1 +1 @@
-{"version":3,"file":"add.js","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAQtE,MAAM,CAAC,KAAK,UAAU,MAAM,CAAC,MAAc,EAAE,IAAgB;IAC3D,MAAM,OAAO,GAAG,uBAAuB,CAAC;QACtC,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,SAAS,EAAE,IAAI,CAAC,SAAS;KAC1B,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAC/D,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,OAAO,CAAC,KAAK,CAAC,yBAAyB,MAAM,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,OAAO,CAAC,GAAG,CAAC,WAAW,MAAM,CAAC,IAAI,KAAK,MAAM,CAAC,EAAE,KAAK,MAAM,CAAC,OAAO,GAAG,CAAC,CAAC;AAC1E,CAAC"}
+{"version":3,"file":"add.js","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAQtE,MAAM,CAAC,KAAK,UAAU,MAAM,CAAC,MAAc,EAAE,IAAgB;IAC3D,MAAM,OAAO,GAAG,uBAAuB,CAAC;QACtC,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,SAAS,EAAE,IAAI,CAAC,SAAS;KAC1B,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IACnE,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,OAAO,CAAC,KAAK,CAAC,yBAAyB,MAAM,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,OAAO,CAAC,GAAG,CAAC,WAAW,MAAM,CAAC,IAAI,KAAK,MAAM,CAAC,EAAE,KAAK,MAAM,CAAC,OAAO,GAAG,CAAC,CAAC;AAC1E,CAAC"}

package/dist/commands/info.d.ts

@@ -1,5 +1,5 @@
 export interface InfoOptions {
-    version?: string;
+    toolVersion?: string;
     cacheDir?: string;
 }
 export declare function runInfo(toolId: string, opts: InfoOptions): Promise<void>;

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

@@ -1 +1 @@
-{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}
+{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,WAAW;IAC1B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}

package/dist/commands/info.js

@@ -3,7 +3,7 @@ import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 export async function runInfo(toolId, opts) {
     const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    const coords = cache.resolveToolCoordinates(toolId, opts.version);
+    const coords = cache.resolveToolCoordinates(toolId, opts.toolVersion);
     if (coords.version === null) {
         console.error(`No version specified for tool: ${toolId}`);
         process.exitCode = 1;

package/dist/commands/info.js.map

@@ -1 +1 @@
-{"version":3,"file":"info.js","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAOhE,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,MAAc,EAAE,IAAiB;IAC7D,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAClE,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;QAC5B,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC1D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IACjF,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;IACzC,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,EAAE,CAAC,CAAC;QACpD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,GAAG,CAAC,CAAC;IAElF,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IACzC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;IACvC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,SAAS,EAAE,CAAC,CAAC;IACzD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,WAAW,IAAI,EAAE,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACnD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,IAAI,UAAU,EAAE,CAAC;QACf,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,SAAS,EAAE,CAAC,CAAC;IACtD,CAAC;AACH,CAAC"}
+{"version":3,"file":"info.js","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAOhE,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,MAAc,EAAE,IAAiB;IAC7D,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IACtE,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;QAC5B,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC1D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IACjF,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;IACzC,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,EAAE,CAAC,CAAC;QACpD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,GAAG,CAAC,CAAC;IAElF,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IACzC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;IACvC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,SAAS,EAAE,CAAC,CAAC;IACzD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,WAAW,IAAI,EAAE,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACnD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,IAAI,UAAU,EAAE,CAAC;QACf,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,SAAS,EAAE,CAAC,CAAC;IACtD,CAAC;AACH,CAAC"}

package/dist/commands/schema.d.ts

@@ -1,5 +1,5 @@
 export interface SchemaOptions {
-    version?: string;
+    toolVersion?: string;
     representation?: string;
     output?: string;
     cacheDir?: string;

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

@@ -1 +1 @@
-{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAWA,MAAM,WAAW,aAAa;IAC5B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAoDlF"}
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAWA,MAAM,WAAW,aAAa;IAC5B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAoDlF"}

package/dist/commands/schema.js

@@ -13,7 +13,7 @@ export async function runSchema(toolId, opts) {
     const stateRep = repName;
     const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    const result = await loadCachedTool(cache, toolId, opts.version);
+    const result = await loadCachedTool(cache, toolId, opts.toolVersion);
     if (isResolveError(result)) {
         if (result.kind === "no_version") {
             console.error(`No version specified for tool: ${toolId}`);

package/dist/commands/schema.js.map

@@ -1 +1 @@
-{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EACL,gBAAgB,EAChB,qBAAqB,GAGtB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AASnE,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,MAAc,EAAE,IAAmB;IACjE,MAAM,OAAO,GAAG,IAAI,CAAC,cAAc,IAAI,eAAe,CAAC;IACvD,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,OAA8B,CAAC,EAAE,CAAC;QACpE,OAAO,CAAC,KAAK,CACX,2BAA2B,OAAO,gBAAgB,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACrF,CAAC;QACF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,QAAQ,GAAG,OAA8B,CAAC;IAEhD,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IACjE,IAAI,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,IAAI,KAAK,YAAY,EAAE,CAAC;YACjC,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,sCAAsC,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAA6B;QACvC,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,MAAgD;KACzE,CAAC;IAEF,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,QAA+B,CAAC,CAAC;IAC/E,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,2EAA2E,CAAC,CAAC;QAC3F,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,IAAI,UAAmB,CAAC;IACxB,IAAI,CAAC;QACH,UAAU,GAAG,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAC7C,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QACvD,OAAO,CAAC,KAAK,CAAC,kCAAkC,GAAG,EAAE,CAAC,CAAC;QACvD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IAEnD,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,CAAC;AACH,CAAC"}
+{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EACL,gBAAgB,EAChB,qBAAqB,GAGtB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AASnE,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,MAAc,EAAE,IAAmB;IACjE,MAAM,OAAO,GAAG,IAAI,CAAC,cAAc,IAAI,eAAe,CAAC;IACvD,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,OAA8B,CAAC,EAAE,CAAC;QACpE,OAAO,CAAC,KAAK,CACX,2BAA2B,OAAO,gBAAgB,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACrF,CAAC;QACF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,QAAQ,GAAG,OAA8B,CAAC;IAEhD,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IACrE,IAAI,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,IAAI,KAAK,YAAY,EAAE,CAAC;YACjC,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,sCAAsC,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAA6B;QACvC,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,MAAgD;KACzE,CAAC;IAEF,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,QAA+B,CAAC,CAAC;IAC/E,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,2EAA2E,CAAC,CAAC;QAC3F,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,IAAI,UAAmB,CAAC;IACxB,IAAI,CAAC;QACH,UAAU,GAAG,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAC7C,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QACvD,OAAO,CAAC,KAAK,CAAC,kCAAkC,GAAG,EAAE,CAAC,CAAC;QACvD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IAEnD,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,CAAC;AACH,CAAC"}

package/dist/commands/summarize.d.ts

@@ -1,6 +1,6 @@
 import { type ParsedTool } from "@galaxy-tool-util/schema";
 export interface SummarizeOptions {
-    version?: string;
+    toolVersion?: string;
     output?: string;
     cacheDir?: string;
 }

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

@@ -1 +1 @@
-{"version":3,"file":"summarize.d.ts","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAGA,OAAO,EAEL,KAAK,UAAU,EAGhB,MAAM,0BAA0B,CAAC;AAIlC,MAAM,WAAW,gBAAgB;IAC/B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,yBAAyB;IACxC,cAAc,EAAE,CAAC,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE;QACN,IAAI,EAAE,UAAU,GAAG,QAAQ,GAAG,OAAO,GAAG,QAAQ,GAAG,SAAS,CAAC;QAC7D,KAAK,EAAE,MAAM,CAAC;QACd,GAAG,EAAE,MAAM,CAAC;QACZ,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;KAC1B,CAAC;IACF,SAAS,EAAE;QACT,gBAAgB,EAAE,MAAM,CAAC;QACzB,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;KACrC,CAAC;IACF,WAAW,EAAE,UAAU,CAAC;IACxB,aAAa,EAAE;QACb,aAAa,EAAE,OAAO,GAAG,IAAI,CAAC;QAC9B,oBAAoB,EAAE,OAAO,GAAG,IAAI,CAAC;KACtC,CAAC;IACF,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AA+BD,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,gBAAgB,GACrB,OAAO,CAAC,yBAAyB,GAAG,IAAI,CAAC,CAwC3C;AAED,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAUxF"}
+{"version":3,"file":"summarize.d.ts","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAGA,OAAO,EAEL,KAAK,UAAU,EAGhB,MAAM,0BAA0B,CAAC;AAIlC,MAAM,WAAW,gBAAgB;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,yBAAyB;IACxC,cAAc,EAAE,CAAC,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE;QACN,IAAI,EAAE,UAAU,GAAG,QAAQ,GAAG,OAAO,GAAG,QAAQ,GAAG,SAAS,CAAC;QAC7D,KAAK,EAAE,MAAM,CAAC;QACd,GAAG,EAAE,MAAM,CAAC;QACZ,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;KAC1B,CAAC;IACF,SAAS,EAAE;QACT,gBAAgB,EAAE,MAAM,CAAC;QACzB,oBAAoB,EAAE,MAAM,GAAG,IAAI,CAAC;KACrC,CAAC;IACF,WAAW,EAAE,UAAU,CAAC;IACxB,aAAa,EAAE;QACb,aAAa,EAAE,OAAO,GAAG,IAAI,CAAC;QAC9B,oBAAoB,EAAE,OAAO,GAAG,IAAI,CAAC;KACtC,CAAC;IACF,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AA+BD,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,gBAAgB,GACrB,OAAO,CAAC,yBAAyB,GAAG,IAAI,CAAC,CAwC3C;AAED,wBAAsB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAUxF"}

package/dist/commands/summarize.js

@@ -32,7 +32,7 @@ export async function buildToolSummaryManifest(toolId, opts) {
     const cacheDir = getCacheDir(opts.cacheDir);
     const cache = makeNodeToolCache({ cacheDir });
     await cache.index.load();
-    const result = await loadCachedTool(cache, toolId, opts.version);
+    const result = await loadCachedTool(cache, toolId, opts.toolVersion);
     if (isResolveError(result)) {
         if (result.kind === "no_version") {
             console.error(`No version specified for tool: ${toolId}`);

package/dist/commands/summarize.js.map

@@ -1 +1 @@
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+{"version":3,"file":"summarize.js","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EACL,gBAAgB,GAIjB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AA+BnE,SAAS,UAAU,CAAC,KAAyB;IAC3C,IAAI,KAAK,KAAK,KAAK;QAAE,OAAO,UAAU,CAAC;IACvC,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,OAAO,IAAI,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IAChF,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,cAAc,CACrB,IAAgB,EAChB,GAAwB,EACxB,QAAkB;IAElB,MAAM,MAAM,GAA6B;QACvC,UAAU,EAAE,IAAI,CAAC,MAAgD;KAClE,CAAC;IACF,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IACnD,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QAC/B,QAAQ,CAAC,IAAI,CAAC,GAAG,GAAG,oDAAoD,CAAC,CAAC;QAC1E,OAAO,IAAI,CAAC;IACd,CAAC;IACD,IAAI,CAAC;QACH,OAAO,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACvC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,QAAQ,CAAC,IAAI,CACX,GAAG,GAAG,oCAAoC,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAC7F,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,MAAc,EACd,IAAsB;IAEtB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC;IAC9C,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IACrE,IAAI,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,IAAI,KAAK,YAAY,EAAE,CAAC;YACjC,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,sCAAsC,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,SAAS,KAAK,MAAM,CAAC,GAAG,CAAC,CAAC;IACjG,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,QAAQ,GAA8B;QAC1C,cAAc,EAAE,CAAC;QACjB,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,EAAE;QACvB,YAAY,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO;QACjC,SAAS,EAAE,MAAM,CAAC,GAAG;QACrB,MAAM,EAAE;YACN,IAAI,EAAE,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC;YACpC,KAAK,EAAE,UAAU,EAAE,MAAM,IAAI,SAAS;YACtC,GAAG,EAAE,UAAU,EAAE,UAAU,IAAI,EAAE;YACjC,SAAS,EAAE,UAAU,EAAE,SAAS,IAAI,IAAI;SACzC;QACD,SAAS,EAAE;YACT,gBAAgB,EAAE,IAAI,CAAC,QAAQ,EAAE,GAAG,MAAM,CAAC,GAAG,OAAO,CAAC;YACtD,oBAAoB,EAAE,IAAI;SAC3B;QACD,WAAW,EAAE,MAAM,CAAC,IAAI;QACxB,aAAa,EAAE;YACb,aAAa,EAAE,cAAc,CAAC,MAAM,CAAC,IAAI,EAAE,eAAe,EAAE,QAAQ,CAAC;YACrE,oBAAoB,EAAE,cAAc,CAAC,MAAM,CAAC,IAAI,EAAE,sBAAsB,EAAE,QAAQ,CAAC;SACpF;QACD,QAAQ;KACT,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,MAAc,EAAE,IAAsB;IACvE,MAAM,QAAQ,GAAG,MAAM,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAC9D,IAAI,QAAQ,KAAK,IAAI;QAAE,OAAO;IAC9B,MAAM,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC;IACxD,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,sBAAsB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IACnD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAC/B,CAAC;AACH,CAAC"}

package/dist/commands/tool-versions.d.ts

@@ -1,3 +1,5 @@
+import { toTrsToolId } from "@galaxy-tool-util/core";
+export { toTrsToolId };
 export interface ToolVersionsOptions {
     json?: boolean;
     latest?: boolean;
@@ -6,6 +8,5 @@ export interface ToolVersionsJsonOutput {
     trsToolId: string;
     versions: string[];
 }
-export declare function toTrsToolId(input: string): string;
 export declare function runToolVersions(toolId: string, opts: ToolVersionsOptions): Promise<void>;
 //# sourceMappingURL=tool-versions.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"tool-versions.d.ts","sourceRoot":"","sources":["../../src/commands/tool-versions.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,mBAAmB;IAClC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,sBAAsB;IACrC,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAOjD;AAED,wBAAsB,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwD9F"}
+{"version":3,"file":"tool-versions.d.ts","sourceRoot":"","sources":["../../src/commands/tool-versions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAwB,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAI3E,OAAO,EAAE,WAAW,EAAE,CAAC;AAEvB,MAAM,WAAW,mBAAmB;IAClC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,sBAAsB;IACrC,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,wBAAsB,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwD9F"}

package/dist/commands/tool-versions.js

@@ -1,13 +1,7 @@
-import { DEFAULT_TOOLSHED_URL } from "@galaxy-tool-util/core";
+import { DEFAULT_TOOLSHED_URL, toTrsToolId } from "@galaxy-tool-util/core";
 import { ToolFetchError, getTRSToolVersions } from "@galaxy-tool-util/search";
-export function toTrsToolId(input) {
-    if (input.includes("~"))
-        return input;
-    const parts = input.split("/").filter((p) => p.length > 0);
-    if (parts.length === 3)
-        return `${parts[0]}~${parts[1]}~${parts[2]}`;
-    throw new Error(`Invalid tool id: expected \`<owner>~<repo>~<tool_id>\` or \`<owner>/<repo>/<tool_id>\`, got: ${input}`);
-}
+// Re-exported for tool-revisions and tests; canonical impl lives in @galaxy-tool-util/core.
+export { toTrsToolId };
 export async function runToolVersions(toolId, opts) {
     let trsToolId;
     try {

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

@@ -1 +1 @@
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package/dist/commands/validate-workflow-json-schema.d.ts.map

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

@@ -13,24 +13,55 @@ import * as JSONSchema from "effect/JSONSchema";
 import Ajv2020 from "ajv/dist/2020.js";
 import { readFileSync, existsSync } from "node:fs";
 import { join } from "node:path";
-import { buildSingleValidationReport } from "@galaxy-tool-util/schema";
+import { buildSingleValidationReport, SKIP_STATUSES, nativeConnectionsFromFormat2In, } from "@galaxy-tool-util/schema";
+import { isEmptyState } from "./validate-workflow.js";
 import { isResolveError, loadCachedTool } from "./resolve-tool.js";
 const Ajv = Ajv2020.default ?? Ajv2020;
-const ajv = new Ajv({ allErrors: true, strict: false });
+// Recursively drop `$id` keys. Effect's JSONSchema.make inlines unknown/any
+// params as `{$id: "/schemas/unknown", title: "unknown"}` (and `/schemas/any`)
+// — a leaf that matches anything. A tool with two such params emits the same
+// `$id` twice in one schema, and AJV rejects duplicate `$id` registration with
+// "resolves to more than one schema". These ids are inlined (never `$ref`
+// targets) and `$defs` refs use JSON-pointer paths, so stripping `$id` is safe.
+function stripIds(schema) {
+    if (schema === null || typeof schema !== "object")
+        return schema;
+    if (Array.isArray(schema))
+        return schema.map(stripIds);
+    const result = {};
+    for (const [key, value] of Object.entries(schema)) {
+        if (key === "$id")
+            continue;
+        result[key] = stripIds(value);
+    }
+    return result;
+}
+// Compile a schema, stripping `$id` first (see stripIds). Each compile uses a
+// fresh Ajv instance so no cross-schema `$id`/`$ref` state leaks between tools.
+// Validators are cached by callers (module structural singletons +
+// _toolStateCache), so this runs once per unique schema.
+function compileSchema(schema) {
+    const instance = new Ajv({ allErrors: true, strict: false });
+    return instance.compile(stripIds(schema));
+}
 // --- structural schema cache (generated once) ---
 let _nativeStructValidator;
 let _format2StructValidator;
+// Structural validation is non-strict (additionalProperties allowed), matching
+// Python's `_get_structural_validator(strict=False)` default — real workflows
+// carry extra envelope/step keys. The strict-structure axis is a separate path
+// (`checkStrictStructure`, Effect decode with onExcessProperty: "error").
 function nativeStructuralValidator() {
     if (!_nativeStructValidator) {
         const schema = JSONSchema.make(NativeGalaxyWorkflowSchema, { target: "jsonSchema2020-12" });
-        _nativeStructValidator = ajv.compile(schema);
+        _nativeStructValidator = compileSchema(stripAdditionalProperties(schema));
     }
     return _nativeStructValidator;
 }
 function format2StructuralValidator() {
     if (!_format2StructValidator) {
         const schema = JSONSchema.make(GalaxyWorkflowSchema, { target: "jsonSchema2020-12" });
-        _format2StructValidator = ajv.compile(schema);
+        _format2StructValidator = compileSchema(stripAdditionalProperties(schema));
     }
     return _format2StructValidator;
 }
@@ -64,7 +95,7 @@ function buildToolStateValidator(bundle, representation) {
     try {
         const jsonSchema = JSONSchema.make(effectSchema, { target: "jsonSchema2020-12" });
         const relaxed = stripAdditionalProperties(jsonSchema);
-        return ajv.compile(relaxed);
+        return compileSchema(relaxed);
     }
     catch {
         return null;
@@ -82,7 +113,7 @@ function loadToolStateValidatorFromDir(toolId, toolVersion, schemaDir) {
         return null;
     try {
         const raw = JSON.parse(readFileSync(schemaPath, "utf-8"));
-        return ajv.compile(raw);
+        return compileSchema(raw);
     }
     catch {
         return null;
@@ -187,7 +218,7 @@ export async function runValidateWorkflowJsonSchema(filePath, data, format, opts
     let validated = 0;
     let skipped = 0;
     for (const r of results) {
-        if (r.status === "skip_tool_not_found" || r.status === "skip_replacement_params") {
+        if (SKIP_STATUSES.has(r.status)) {
             skipped++;
             console.warn(`  [${r.step}] skipped — ${r.errors[0] ?? "unknown"}`);
         }
@@ -244,7 +275,21 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     const bundle = {
         parameters: resolved.tool.inputs,
     };
-    const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
+    const connections = {};
+    for (const [k, v] of Object.entries(step.input_connections)) {
+        connections[k] = v;
+    }
+    return _validateNativeStateJsonSchema(bundle, step.tool_state, connections, stepLabel, toolId, toolVersion, toolSchemaDir);
+}
+/**
+ * Validate a native-encoded tool_state block against the `workflow_step_native`
+ * JSON Schema. Shared by native-body steps and format2-body steps carrying a
+ * verbatim `tool_state` block — same encoding, same validator regardless of
+ * workflow format. (JSON Schema can't enforce double-encoded scalar types, e.g.
+ * "5" for an int, but still checks structure and unknown keys.)
+ */
+function _validateNativeStateJsonSchema(bundle, toolState, connections, stepLabel, toolId, toolVersion, toolSchemaDir) {
+    const replacementScan = scanForReplacements(bundle.parameters, toolState);
     if (replacementScan === "yes") {
         return {
             step: stepLabel,
@@ -254,11 +299,7 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
             errors: ["replacement parameters detected"],
         };
     }
-    const state = structuredClone(step.tool_state);
-    const connections = {};
-    for (const [k, v] of Object.entries(step.input_connections)) {
-        connections[k] = v;
-    }
+    const state = structuredClone(toolState);
     injectConnectionsIntoState(bundle.parameters, state, connections);
     const validate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_native", toolSchemaDir);
     if (!validate) {
@@ -321,8 +362,13 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     const bundle = {
         parameters: resolved.tool.inputs,
     };
-    const rawState = step.state ?? step.tool_state ?? {};
-    const state = rawState;
+    // A verbatim native `tool_state` block validates through the native path
+    // (same encoding regardless of workflow format); a schema-aware `state` block
+    // validates below. State shape — not workflow format — picks the validator.
+    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 baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
     if (!baseValidate) {
@@ -355,17 +401,12 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     // Level 2: linked validation with connections injected
     if (Object.keys(connections).length > 0) {
         const linkedState = structuredClone(state);
-        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections);
-        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}"`),
-            };
-        }
+        // 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 {

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

@@ -1 +1 @@
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package/dist/commands/validate-workflow.d.ts

@@ -13,6 +13,8 @@ export interface ValidateWorkflowOptions extends StrictOptions {
     reportHtml?: string | boolean;
     connections?: boolean;
 }
+/** A state field is "empty" when null/undefined or an object with no keys (mirrors Python `not step.state`). */
+export declare function isEmptyState(value: unknown): boolean;
 /** Run Effect Schema decode on raw workflow data and return structural decode failures. */
 export declare function decodeStructureErrors(data: Record<string, unknown>, format: WorkflowFormat): string[];
 export type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";

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

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

@@ -1,5 +1,5 @@
 import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
-import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, 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, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
 import * as ParseResult from "effect/ParseResult";
 import * as S from "effect/Schema";
 import { dirname } from "node:path";
@@ -14,6 +14,10 @@ function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
     return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
 }
+/** A state field is "empty" when null/undefined or an object with no keys (mirrors Python `not step.state`). */
+export function isEmptyState(value) {
+    return value == null || Object.keys(value).length === 0;
+}
 /** Run Effect Schema decode on raw workflow data and return structural decode failures. */
 export function decodeStructureErrors(data, format) {
     const cls = format === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
@@ -222,8 +226,22 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache)
     const bundle = {
         parameters: resolved.tool.inputs,
     };
+    const connections = {};
+    for (const [key, val] of Object.entries(step.input_connections)) {
+        connections[key] = val;
+    }
+    return _validateNativeState(bundle, step.tool_state, connections, stepLabel, toolId, toolVersion);
+}
+/**
+ * Validate a native-encoded tool_state block against the `workflow_step_native`
+ * model. Shared by native-body steps and format2-body steps that carry a
+ * verbatim `tool_state` block instead of a schema-aware `state` block — the
+ * encoding (double-encoded scalars, inline ConnectedValue/RuntimeValue markers)
+ * is identical regardless of workflow format, so the same model validates both.
+ */
+function _validateNativeState(bundle, toolState, connections, stepLabel, toolId, toolVersion) {
     // Skip validation if replacement parameters (${...}) are present in typed fields
-    const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
+    const replacementScan = scanForReplacements(bundle.parameters, toolState);
     if (replacementScan === "yes") {
         return {
             step: stepLabel,
@@ -234,13 +252,8 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache)
         };
     }
     // Deep copy state and inject connection markers
-    const state = structuredClone(step.tool_state);
-    const connections = {};
-    for (const [key, val] of Object.entries(step.input_connections)) {
-        connections[key] = val;
-    }
+    const state = structuredClone(toolState);
     injectConnectionsIntoState(bundle.parameters, state, connections);
-    // Validate against workflow_step_native schema
     const fieldModel = createFieldModel(bundle, "workflow_step_native");
     if (!fieldModel) {
         return {
@@ -306,10 +319,17 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache)
     const bundle = {
         parameters: resolved.tool.inputs,
     };
-    // Get state from step.state or step.tool_state.
-    // 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 ?? step.tool_state ?? {}));
+    // 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);
+    }
+    // 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 baseModel = createFieldModel(bundle, "workflow_step");
@@ -346,7 +366,9 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache)
     // 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);
+        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
+            linked: true,
+        });
         const unmatchedKeys = Object.keys(remaining);
         if (unmatchedKeys.length > 0) {
             return {

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package/dist/spec/build-program.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build-program.d.ts","sourceRoot":"","sources":["../../src/spec/build-program.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,KAAK,EAAE,WAAW,EAA2B,MAAM,uBAAuB,CAAC;AAElF,MAAM,MAAM,SAAS,GAAG,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;AACjE,MAAM,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;AAExD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,GAAG,OAAO,CAS1F"}
+{"version":3,"file":"build-program.d.ts","sourceRoot":"","sources":["../../src/spec/build-program.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,KAAK,EAAE,WAAW,EAA2B,MAAM,uBAAuB,CAAC;AAElF,MAAM,MAAM,SAAS,GAAG,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;AACjE,MAAM,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;AAUxD,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,GAAG,OAAO,CAS1F"}

package/dist/spec/build-program.js

@@ -5,6 +5,13 @@
  * runtime action functions.
  */
 import { Command } from "commander";
+/**
+ * Attribute names commander reserves for its built-in flags. `.version()`
+ * registers `--version` on the program (and it propagates to subcommands);
+ * `--help` is auto-added to every command. A spec data option with either
+ * name silently triggers the built-in action instead of binding a value.
+ */
+const RESERVED_OPTION_NAMES = new Set(["version", "help"]);
 export function buildProgramFromSpec(spec, handlers) {
     validateSpec(spec, handlers);
     const program = new Command();
@@ -35,6 +42,11 @@ function validateSpec(spec, handlers) {
         const seenOptions = new Set();
         const checkOptName = (flags) => {
             const optName = attributeNameFromFlags(flags);
+            if (RESERVED_OPTION_NAMES.has(optName)) {
+                throw new Error(`Option "--${optName}" on command "${cmd.name}" collides with commander's built-in ` +
+                    `--${optName} flag (it would silently trigger ${optName === "version" ? "the version" : "the help"} ` +
+                    `action instead of binding). Rename it (e.g. --tool-version).`);
+            }
             if (seenOptions.has(optName)) {
                 throw new Error(`Duplicate option "${optName}" on command "${cmd.name}"`);
             }

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.6.0",
+  "version": "1.7.1",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -39,10 +39,10 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/connection-validation": "1.6.0",
-    "@galaxy-tool-util/core": "1.6.0",
-    "@galaxy-tool-util/schema": "1.6.0",
-    "@galaxy-tool-util/search": "1.6.0"
+    "@galaxy-tool-util/connection-validation": "1.7.1",
+    "@galaxy-tool-util/core": "1.7.1",
+    "@galaxy-tool-util/schema": "1.7.1",
+    "@galaxy-tool-util/search": "1.7.1"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",

package/spec/galaxy-tool-cache.json

@@ -15,7 +15,7 @@
       ],
       "options": [
         {
-          "flags": "--version <ver>",
+          "flags": "--tool-version <ver>",
           "description": "Tool version"
         },
         {
@@ -55,7 +55,7 @@
       ],
       "options": [
         {
-          "flags": "--version <ver>",
+          "flags": "--tool-version <ver>",
           "description": "Tool version"
         },
         {
@@ -93,7 +93,7 @@
       ],
       "options": [
         {
-          "flags": "--version <ver>",
+          "flags": "--tool-version <ver>",
           "description": "Tool version"
         },
         {
@@ -123,7 +123,7 @@
       ],
       "options": [
         {
-          "flags": "--version <ver>",
+          "flags": "--tool-version <ver>",
           "description": "Tool version"
         },
         {