@galaxy-tool-util/cli 1.0.0 → 1.1.0

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

@@ -1,65 +1,4 @@
 #!/usr/bin/env node
-import { Command } from "commander";
-import { runAdd } from "../commands/add.js";
-import { runList } from "../commands/list.js";
-import { runInfo } from "../commands/info.js";
-import { runClear } from "../commands/clear.js";
-import { runPopulateWorkflow } from "../commands/populate-workflow.js";
-import { runSchema } from "../commands/schema.js";
-import { runStructuralSchema } from "../commands/structural-schema.js";
-const program = new Command();
-program
-    .name("galaxy-tool-cache")
-    .description("Cache and inspect Galaxy tool metadata")
-    .version("1.0.0");
-program
-    .command("add")
-    .description("Fetch a tool from ToolShed/Galaxy and cache it")
-    .argument("<tool_id>", "Tool ID (full toolshed path or TRS ID)")
-    .option("--version <ver>", "Tool version")
-    .option("--cache-dir <dir>", "Cache directory")
-    .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
-    .action(runAdd);
-program
-    .command("list")
-    .description("List cached tools")
-    .option("--json", "Output as JSON")
-    .option("--cache-dir <dir>", "Cache directory")
-    .action(runList);
-program
-    .command("info")
-    .description("Show metadata for a cached tool")
-    .argument("<tool_id>", "Tool ID")
-    .option("--version <ver>", "Tool version")
-    .option("--cache-dir <dir>", "Cache directory")
-    .action(runInfo);
-program
-    .command("clear")
-    .description("Clear cached tools")
-    .argument("[prefix]", "Only clear tools matching this prefix")
-    .option("--cache-dir <dir>", "Cache directory")
-    .action(runClear);
-program
-    .command("schema")
-    .description("Export JSON Schema for a cached tool's parameters")
-    .argument("<tool_id>", "Tool ID")
-    .option("--version <ver>", "Tool version")
-    .option("--representation <rep>", "State representation (e.g., workflow_step)", "workflow_step")
-    .option("--output <file>", "Output file (default: stdout)")
-    .option("--cache-dir <dir>", "Cache directory")
-    .action(runSchema);
-program
-    .command("populate-workflow")
-    .description("Scan a workflow and cache all referenced tools")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--cache-dir <dir>", "Cache directory")
-    .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
-    .action(runPopulateWorkflow);
-program
-    .command("structural-schema")
-    .description("Export the structural JSON Schema for Galaxy workflows")
-    .option("--format <fmt>", "Workflow format: format2 (default) or native", "format2")
-    .option("--output <file>", "Output file (default: stdout)")
-    .action(runStructuralSchema);
-program.parse();
+import { buildGalaxyToolCacheProgram } from "../programs/galaxy-tool-cache.js";
+buildGalaxyToolCacheProgram().parse();
 //# sourceMappingURL=galaxy-tool-cache.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"galaxy-tool-cache.js","sourceRoot":"","sources":["../../src/bin/galaxy-tool-cache.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,2BAA2B,EAAE,MAAM,kCAAkC,CAAC;AAE/E,2BAA2B,EAAE,CAAC,KAAK,EAAE,CAAC"}

package/dist/bin/gxwf.js

@@ -1,158 +1,4 @@
 #!/usr/bin/env node
-import { Command } from "commander";
-import { runClean } from "../commands/clean.js";
-import { runCleanTree } from "../commands/clean-tree.js";
-import { runConvert } from "../commands/convert.js";
-import { runConvertTree } from "../commands/convert-tree.js";
-import { runRoundtrip } from "../commands/roundtrip.js";
-import { runRoundtripTree } from "../commands/roundtrip-tree.js";
-import { runLint } from "../commands/lint.js";
-import { runMermaid } from "../commands/mermaid.js";
-import { runLintTree } from "../commands/lint-tree.js";
-import { runValidateWorkflow } from "../commands/validate-workflow.js";
-import { runValidateTests } from "../commands/validate-tests.js";
-import { runValidateTestsTree } from "../commands/validate-tests-tree.js";
-import { runValidateTree } from "../commands/validate-tree.js";
-import { addStrictOptions } from "../commands/strict-options.js";
-const program = new Command();
-program
-    .name("gxwf")
-    .description("Galaxy workflow operations — validate, clean, lint, convert (single-file and tree)")
-    .version("1.0.0");
-addStrictOptions(program
-    .command("validate")
-    .description("Validate Galaxy workflow files (structure + optional tool state)")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--no-tool-state", "Skip tool state validation")
-    .option("--cache-dir <dir>", "Tool cache directory")
-    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
-    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
-    .option("--json", "Output structured JSON report")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateWorkflow);
-program
-    .command("validate-tests")
-    .description("Validate a workflow-test file (*-tests.yml, *.gxwf-tests.yml) against the Galaxy Tests schema")
-    .argument("<file>", "Tests file (*-tests.yml)")
-    .option("--json", "Output structured JSON report")
-    .option("--workflow <path>", "Cross-check job inputs + output assertions against a workflow (.ga / .gxwf.yml)")
-    .action(runValidateTests);
-program
-    .command("clean")
-    .description("Strip stale keys and decode legacy tool_state encoding")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--output <file>", "Write cleaned workflow to file (default: stdout)")
-    .option("--diff", "Show diff of changes instead of writing output")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--json", "Output structured JSON report")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
-    .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
-    .action(runClean);
-addStrictOptions(program
-    .command("lint")
-    .description("Lint Galaxy workflow — structural checks, best practices, tool state validation")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
-    .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
-    .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--json", "Output structured JSON result")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLint);
-addStrictOptions(program
-    .command("convert")
-    .description("Convert between native (.ga) and format2 (.gxwf.yml) formats")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
-    .option("--output <file>", "Write result to file (default: stdout)")
-    .option("--compact", "Omit position info in format2 output")
-    .option("--json", "Force JSON output")
-    .option("--yaml", "Force YAML output")
-    .option("--format <fmt>", "Force source format (auto-detected by default)")
-    .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
-    .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvert);
-addStrictOptions(program
-    .command("roundtrip")
-    .description("Roundtrip-validate a native workflow: native → format2 → native, diff tool_state")
-    .argument("<file>", "Native workflow file (.ga)")
-    .option("--cache-dir <dir>", "Tool cache directory")
-    .option("--format <fmt>", "Force source format (must resolve to native)")
-    .option("--json", "Output structured JSON report")
-    .option("--errors-only", "Suppress benign diffs and clean steps from output")
-    .option("--benign-only", "Show only steps with benign diffs (no errors, no failures)")
-    .option("--brief", "Omit per-diff list; show only the one-line summary")).action(runRoundtrip);
-program
-    .command("mermaid")
-    .description("Render a Galaxy workflow as a Mermaid flowchart diagram")
-    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
-    .argument("[output]", "Output path (.mmd for raw, .md for fenced code block); stdout if omitted")
-    .option("--comments", "Render frame comments as Mermaid subgraphs")
-    .action((file, output, opts) => runMermaid(file, { output, comments: opts.comments }));
-// -- Tree (batch) variants --
-addStrictOptions(program
-    .command("validate-tree")
-    .description("Batch validate all workflows under a directory")
-    .argument("<dir>", "Directory to scan for workflows")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--no-tool-state", "Skip tool state validation")
-    .option("--cache-dir <dir>", "Tool cache directory")
-    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
-    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
-    .option("--json", "Output structured JSON report")
-    .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateTree);
-addStrictOptions(program
-    .command("lint-tree")
-    .description("Batch lint all workflows under a directory")
-    .argument("<dir>", "Directory to scan for workflows")
-    .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
-    .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
-    .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--json", "Output structured JSON report")
-    .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLintTree);
-program
-    .command("clean-tree")
-    .description("Batch clean all workflows under a directory")
-    .argument("<dir>", "Directory to scan for workflows")
-    .option("--output-dir <dir>", "Write cleaned workflows to directory (mirrors source tree)")
-    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
-    .option("--json", "Output structured JSON report")
-    .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
-    .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
-    .action(runCleanTree);
-addStrictOptions(program
-    .command("convert-tree")
-    .description("Batch convert all workflows under a directory")
-    .argument("<dir>", "Directory to scan for workflows")
-    .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
-    .option("--output-dir <dir>", "Write converted workflows to directory (required)")
-    .option("--compact", "Omit position info in format2 output")
-    .option("--report-json", "Output structured JSON report")
-    .option("--json", "Force JSON output for converted files")
-    .option("--yaml", "Force YAML output")
-    .option("--format <fmt>", "Force source format (auto-detected by default)")
-    .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
-    .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvertTree);
-addStrictOptions(program
-    .command("roundtrip-tree")
-    .description("Batch roundtrip-validate native workflows under a directory")
-    .argument("<dir>", "Directory to scan for native workflows")
-    .option("--cache-dir <dir>", "Tool cache directory")
-    .option("--format <fmt>", "Force source format (must resolve to native)")
-    .option("--json", "Output structured JSON report")
-    .option("--errors-only", "List only files with errors or failures")
-    .option("--benign-only", "List only files with benign diffs (no errors, no failures)")
-    .option("--brief", "Omit per-file lines; print only the aggregate summary")
-    .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
-    .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runRoundtripTree);
-program
-    .command("validate-tests-tree")
-    .description("Batch validate workflow-test files (*-tests.yml / *.gxwf-tests.yml) under a directory")
-    .argument("<dir>", "Directory to scan for test files")
-    .option("--json", "Output structured JSON report")
-    .option("--auto-workflow", "Pair each tests file with a sibling workflow by filename convention (foo.gxwf-tests.yml ↔ foo.gxwf.yml/foo.ga) and cross-check inputs/outputs")
-    .action(runValidateTestsTree);
-program.parse();
+import { buildGxwfProgram } from "../programs/gxwf.js";
+buildGxwfProgram().parse();
 //# sourceMappingURL=gxwf.js.map

package/dist/bin/gxwf.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gxwf.js","sourceRoot":"","sources":["../../src/bin/gxwf.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAEvD,gBAAgB,EAAE,CAAC,KAAK,EAAE,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/commands/lint.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAQL,KAAK,UAAU,EAGf,KAAK,oBAAoB,IAAI,oBAAoB,EAClD,MAAM,0BAA0B,CAAC;AAKlC,OAAO,EAEL,KAAK,aAAa,EAClB,KAAK,qBAAqB,EAC3B,MAAM,qBAAqB,CAAC;AAS7B,MAAM,WAAW,WAAY,SAAQ,aAAa;IAChD,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;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC/B;AAED,MAAM,WAAW,iBAAiB;IAChC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,MAAM,CAAC,EAAE,qBAAqB,CAAC;CAChC;AAED,MAAM,WAAW,UAAU;IACzB,UAAU,EAAE,UAAU,CAAC;IACvB,aAAa,EAAE,UAAU,GAAG,IAAI,CAAC;IACjC,eAAe,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAC;IAC/C,YAAY,EAAE,OAAO,CAAC;IACtB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,EAAE,MAAM,CAAC;CAClB;AAaD,wBAAsB,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA4GhF;AAED,+EAA+E;AAC/E,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,UAAU,CAAC,CA8ErB"}
+{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/commands/lint.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAQL,KAAK,UAAU,EAGf,KAAK,oBAAoB,IAAI,oBAAoB,EAClD,MAAM,0BAA0B,CAAC;AAKlC,OAAO,EAEL,KAAK,aAAa,EAClB,KAAK,qBAAqB,EAC3B,MAAM,qBAAqB,CAAC;AAS7B,MAAM,WAAW,WAAY,SAAQ,aAAa;IAChD,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;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC/B;AAED,MAAM,WAAW,iBAAiB;IAChC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,MAAM,CAAC,EAAE,qBAAqB,CAAC;CAChC;AAED,MAAM,WAAW,UAAU;IACzB,UAAU,EAAE,UAAU,CAAC;IACvB,aAAa,EAAE,UAAU,GAAG,IAAI,CAAC;IACjC,eAAe,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAC;IAC/C,YAAY,EAAE,OAAO,CAAC;IACtB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,EAAE,MAAM,CAAC;CAClB;AAaD,wBAAsB,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAyHhF;AAED,+EAA+E;AAC/E,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,UAAU,CAAC,CA8ErB"}

package/dist/commands/lint.js

@@ -45,6 +45,14 @@ export async function runLint(filePath, opts) {
     if (opts.json || opts.reportHtml) {
         const lintErrors = report.structural.error_count + (report.bestPractices?.error_count ?? 0);
         const lintWarnings = report.structural.warn_count + (report.bestPractices?.warn_count ?? 0);
+        const lintErrorMessages = [
+            ...report.structural.errors.map((m) => m.message),
+            ...(report.bestPractices?.errors.map((m) => m.message) ?? []),
+        ];
+        const lintWarningMessages = [
+            ...report.structural.warnings.map((m) => m.message),
+            ...(report.bestPractices?.warnings.map((m) => m.message) ?? []),
+        ];
         // Effect Schema decode for structure_errors
         const structureErrors = decodeStructureErrors(data, format);
         // Legacy encoding detection for encoding_errors
@@ -55,7 +63,12 @@ export async function runLint(filePath, opts) {
             };
             encodingErrors = await detectEncodingErrors(data, cache, format, expansionOpts);
         }
-        const singleReport = buildSingleLintReport(filePath, lintErrors, lintWarnings, report.stateValidation ?? [], { structure_errors: structureErrors, encoding_errors: encodingErrors });
+        const singleReport = buildSingleLintReport(filePath, lintErrors, lintWarnings, report.stateValidation ?? [], {
+            structure_errors: structureErrors,
+            encoding_errors: encodingErrors,
+            lint_error_messages: lintErrorMessages,
+            lint_warning_messages: lintWarningMessages,
+        });
         if (opts.json) {
             console.log(JSON.stringify(singleReport, null, 2));
         }

package/dist/commands/lint.js.map

@@ -1 +1 @@
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package/dist/commands/repo-search.d.ts

@@ -0,0 +1,31 @@
+export interface RepoSearchOptions {
+    pageSize?: string | number;
+    maxResults?: string | number;
+    page?: string | number;
+    owner?: string;
+    category?: string;
+    json?: boolean;
+}
+export interface NormalizedRepoHit {
+    toolshedUrl: string;
+    repoId: string;
+    repoName: string;
+    repoOwnerUsername: string;
+    description: string | null;
+    homepageUrl: string | null;
+    remoteRepositoryUrl: string | null;
+    categories: string[];
+    approved: boolean;
+    timesDownloaded: number;
+    score: number;
+}
+export interface RepoSearchJsonOutput {
+    query: string;
+    filters: {
+        owner?: string;
+        category?: string;
+    };
+    hits: NormalizedRepoHit[];
+}
+export declare function runRepoSearch(query: string, opts: RepoSearchOptions): Promise<void>;
+//# sourceMappingURL=repo-search.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"repo-search.d.ts","sourceRoot":"","sources":["../../src/commands/repo-search.ts"],"names":[],"mappings":"AAIA,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,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,mBAAmB,EAAE,MAAM,GAAG,IAAI,CAAC;IACnC,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,QAAQ,EAAE,OAAO,CAAC;IAClB,eAAe,EAAE,MAAM,CAAC;IACxB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,QAAQ,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/C,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAgCD,wBAAsB,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4CzF"}

package/dist/commands/repo-search.js

@@ -0,0 +1,100 @@
+import { DEFAULT_TOOLSHED_URL } from "@galaxy-tool-util/core";
+import { ToolFetchError, iterateRepoSearchPages } from "@galaxy-tool-util/search";
+function toInt(value, fallback) {
+    if (value === undefined)
+        return fallback;
+    const n = typeof value === "number" ? value : parseInt(value, 10);
+    return Number.isFinite(n) && n > 0 ? n : fallback;
+}
+function normalize(hit, toolshedUrl) {
+    const r = hit.repository;
+    const categories = r.categories === null
+        ? []
+        : r.categories
+            .split(",")
+            .map((c) => c.trim())
+            .filter((c) => c.length > 0);
+    return {
+        toolshedUrl,
+        repoId: r.id,
+        repoName: r.name,
+        repoOwnerUsername: r.repo_owner_username,
+        description: r.description,
+        homepageUrl: r.homepage_url,
+        remoteRepositoryUrl: r.remote_repository_url,
+        categories,
+        approved: r.approved,
+        timesDownloaded: r.times_downloaded,
+        score: hit.score,
+    };
+}
+export async function runRepoSearch(query, opts) {
+    const pageSize = toInt(opts.pageSize, 20);
+    const maxResults = toInt(opts.maxResults, 50);
+    const page = toInt(opts.page, 1);
+    const toolshedUrl = DEFAULT_TOOLSHED_URL;
+    const hits = [];
+    try {
+        for await (const pageResults of iterateRepoSearchPages(toolshedUrl, query, {
+            pageSize,
+            page,
+            owner: opts.owner,
+            category: opts.category,
+        })) {
+            for (const raw of pageResults.hits) {
+                hits.push(normalize(raw, toolshedUrl));
+                if (hits.length >= maxResults)
+                    break;
+            }
+            if (hits.length >= maxResults)
+                break;
+        }
+    }
+    catch (err) {
+        if (err instanceof ToolFetchError) {
+            console.error(`Tool Shed repo search failed: ${err.message}`);
+            process.exitCode = 3;
+            return;
+        }
+        throw err;
+    }
+    hits.sort((a, b) => b.score - a.score);
+    if (opts.json) {
+        const filters = {};
+        if (opts.owner)
+            filters.owner = opts.owner;
+        if (opts.category)
+            filters.category = opts.category;
+        const envelope = { query, filters, hits };
+        console.log(JSON.stringify(envelope, null, 2));
+    }
+    else if (hits.length === 0) {
+        console.error(`No repos for query: ${query}`);
+    }
+    else {
+        console.log(formatTable(hits));
+    }
+    if (hits.length === 0)
+        process.exitCode = 2;
+}
+function formatTable(hits) {
+    const header = ["score", "downloads", "owner/repo", "categories", "description"];
+    const rows = hits.map((h) => [
+        h.score.toFixed(2),
+        String(h.timesDownloaded),
+        `${h.repoOwnerUsername}/${h.repoName}`,
+        h.categories.join(",") || "-",
+        truncate(h.description ?? "", 60),
+    ]);
+    const widths = header.map((col, i) => Math.max(col.length, ...rows.map((r) => r[i].length)));
+    const fmt = (cells) => cells
+        .map((c, i) => c.padEnd(widths[i]))
+        .join("  ")
+        .trimEnd();
+    return [fmt(header), fmt(widths.map((w) => "-".repeat(w))), ...rows.map(fmt)].join("\n");
+}
+function truncate(s, max) {
+    const flat = s.replace(/\s+/g, " ").trim();
+    return flat.length > max ? `${flat.slice(0, max - 1)}…` : flat;
+}
+//# sourceMappingURL=repo-search.js.map

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

@@ -0,0 +1 @@
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package/dist/commands/tool-revisions.d.ts

@@ -0,0 +1,15 @@
+export interface ToolRevisionsOptions {
+    toolVersion?: string;
+    latest?: boolean;
+    json?: boolean;
+}
+export interface ToolRevisionsJsonOutput {
+    trsToolId: string;
+    version?: string;
+    revisions: {
+        changesetRevision: string;
+        toolVersion: string;
+    }[];
+}
+export declare function runToolRevisions(toolId: string, opts: ToolRevisionsOptions): Promise<void>;
+//# sourceMappingURL=tool-revisions.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/commands/tool-revisions.js

@@ -0,0 +1,56 @@
+import { DEFAULT_TOOLSHED_URL } from "@galaxy-tool-util/core";
+import { ToolFetchError, getToolRevisions } from "@galaxy-tool-util/search";
+import { toTrsToolId } from "./tool-versions.js";
+export async function runToolRevisions(toolId, opts) {
+    let trsToolId;
+    try {
+        trsToolId = toTrsToolId(toolId);
+    }
+    catch (err) {
+        console.error(err.message);
+        process.exitCode = 1;
+        return;
+    }
+    const [owner, repo, xmlToolId] = trsToolId.split("~");
+    let matches;
+    try {
+        matches = await getToolRevisions(DEFAULT_TOOLSHED_URL, {
+            owner,
+            repo,
+            toolId: xmlToolId,
+            version: opts.toolVersion,
+        });
+    }
+    catch (err) {
+        if (err instanceof ToolFetchError) {
+            console.error(`Tool Shed request failed: ${err.message}`);
+            process.exitCode = 3;
+            return;
+        }
+        throw err;
+    }
+    const selected = opts.latest ? matches.slice(-1) : matches;
+    const revisions = selected.map((m) => ({
+        changesetRevision: m.changesetRevision,
+        toolVersion: m.toolVersion,
+    }));
+    if (opts.json) {
+        const envelope = {
+            trsToolId,
+            ...(opts.toolVersion !== undefined ? { version: opts.toolVersion } : {}),
+            revisions,
+        };
+        console.log(JSON.stringify(envelope, null, 2));
+    }
+    else if (revisions.length === 0) {
+        const suffix = opts.toolVersion ? ` at version ${opts.toolVersion}` : "";
+        console.error(`No revisions found for ${trsToolId}${suffix}`);
+    }
+    else {
+        for (const r of revisions)
+            console.log(`${r.changesetRevision}\t${r.toolVersion}`);
+    }
+    if (revisions.length === 0)
+        process.exitCode = 2;
+}
+//# sourceMappingURL=tool-revisions.js.map

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

@@ -0,0 +1 @@
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package/dist/commands/tool-search.d.ts

@@ -0,0 +1,17 @@
+import type { NormalizedToolHit } from "@galaxy-tool-util/search";
+export interface ToolSearchOptions {
+    pageSize?: string | number;
+    maxResults?: string | number;
+    page?: string | number;
+    owner?: string;
+    matchName?: boolean;
+    json?: boolean;
+    enrich?: boolean;
+    cacheDir?: string;
+}
+export interface ToolSearchJsonOutput {
+    query: string;
+    hits: NormalizedToolHit[];
+}
+export declare function runToolSearch(query: string, opts: ToolSearchOptions): Promise<void>;
+//# sourceMappingURL=tool-search.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/commands/tool-search.js

@@ -0,0 +1,107 @@
+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";
+function toInt(value, fallback) {
+    if (value === undefined)
+        return fallback;
+    const n = typeof value === "number" ? value : parseInt(value, 10);
+    return Number.isFinite(n) && n > 0 ? n : fallback;
+}
+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 = [];
+    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;
+        }
+    }
+    catch (err) {
+        if (err instanceof ToolFetchError) {
+            console.error(`Tool Shed search failed: ${err.message}`);
+            process.exitCode = 3;
+            return;
+        }
+        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));
+    }
+    else if (hits.length === 0) {
+        console.error(`No hits for query: ${query}`);
+    }
+    else {
+        console.log(formatTable(hits));
+    }
+    if (hits.length === 0) {
+        process.exitCode = 2;
+    }
+}
+function formatTable(hits) {
+    const header = ["score", "owner/repo", "tool_id", "name", "description"];
+    const rows = hits.map((h) => [
+        h.score.toFixed(2),
+        `${h.repoOwnerUsername}/${h.repoName}`,
+        h.toolId,
+        h.toolName,
+        truncate(h.toolDescription ?? "", 60),
+    ]);
+    const widths = header.map((col, i) => Math.max(col.length, ...rows.map((r) => r[i].length)));
+    const fmt = (cells) => cells
+        .map((c, i) => c.padEnd(widths[i]))
+        .join("  ")
+        .trimEnd();
+    return [fmt(header), fmt(widths.map((w) => "-".repeat(w))), ...rows.map(fmt)].join("\n");
+}
+function truncate(s, max) {
+    const flat = s.replace(/\s+/g, " ").trim();
+    return flat.length > max ? `${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

@@ -0,0 +1 @@
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package/dist/commands/tool-versions.d.ts

@@ -0,0 +1,11 @@
+export interface ToolVersionsOptions {
+    json?: boolean;
+    latest?: boolean;
+}
+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

@@ -0,0 +1 @@
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package/dist/commands/tool-versions.js

@@ -0,0 +1,70 @@
+import { DEFAULT_TOOLSHED_URL } 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}`);
+}
+export async function runToolVersions(toolId, opts) {
+    let trsToolId;
+    try {
+        trsToolId = toTrsToolId(toolId);
+    }
+    catch (err) {
+        console.error(err.message);
+        process.exitCode = 1;
+        return;
+    }
+    let rawVersions;
+    try {
+        rawVersions = await getTRSToolVersions(DEFAULT_TOOLSHED_URL, trsToolId);
+    }
+    catch (err) {
+        if (err instanceof ToolFetchError) {
+            console.error(`TRS request failed: ${err.message}`);
+            process.exitCode = 3;
+            return;
+        }
+        throw err;
+    }
+    // Tool Shed returns oldest-first; we emit newest-last (pass-through).
+    const versions = rawVersions.map((v) => v.id);
+    if (opts.latest) {
+        const latest = versions[versions.length - 1];
+        if (latest === undefined) {
+            if (opts.json) {
+                console.log(JSON.stringify({ trsToolId, versions: [] }, null, 2));
+            }
+            else {
+                console.error(`No versions published for ${trsToolId}`);
+            }
+            process.exitCode = 2;
+            return;
+        }
+        if (opts.json) {
+            console.log(JSON.stringify({ trsToolId, versions: [latest] }, null, 2));
+        }
+        else {
+            console.log(latest);
+        }
+        return;
+    }
+    if (opts.json) {
+        const envelope = { trsToolId, versions };
+        console.log(JSON.stringify(envelope, null, 2));
+    }
+    else if (versions.length === 0) {
+        console.error(`No versions published for ${trsToolId}`);
+    }
+    else {
+        for (const v of versions)
+            console.log(v);
+    }
+    if (versions.length === 0) {
+        process.exitCode = 2;
+    }
+}
+//# sourceMappingURL=tool-versions.js.map

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

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package/dist/programs/galaxy-tool-cache.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare function buildGalaxyToolCacheProgram(): Command;
+//# sourceMappingURL=galaxy-tool-cache.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"galaxy-tool-cache.d.ts","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AASpC,wBAAgB,2BAA2B,IAAI,OAAO,CAiErD"}

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

@@ -0,0 +1,66 @@
+import { Command } from "commander";
+import { runAdd } from "../commands/add.js";
+import { runList } from "../commands/list.js";
+import { runInfo } from "../commands/info.js";
+import { runClear } from "../commands/clear.js";
+import { runPopulateWorkflow } from "../commands/populate-workflow.js";
+import { runSchema } from "../commands/schema.js";
+import { runStructuralSchema } from "../commands/structural-schema.js";
+export function buildGalaxyToolCacheProgram() {
+    const program = new Command();
+    program
+        .name("galaxy-tool-cache")
+        .description("Cache and inspect Galaxy tool metadata")
+        .version("1.0.0");
+    program
+        .command("add")
+        .description("Fetch a tool from ToolShed/Galaxy and cache it")
+        .argument("<tool_id>", "Tool ID (full toolshed path or TRS ID)")
+        .option("--version <ver>", "Tool version")
+        .option("--cache-dir <dir>", "Cache directory")
+        .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
+        .action(runAdd);
+    program
+        .command("list")
+        .description("List cached tools")
+        .option("--json", "Output as JSON")
+        .option("--cache-dir <dir>", "Cache directory")
+        .action(runList);
+    program
+        .command("info")
+        .description("Show metadata for a cached tool")
+        .argument("<tool_id>", "Tool ID")
+        .option("--version <ver>", "Tool version")
+        .option("--cache-dir <dir>", "Cache directory")
+        .action(runInfo);
+    program
+        .command("clear")
+        .description("Clear cached tools")
+        .argument("[prefix]", "Only clear tools matching this prefix")
+        .option("--cache-dir <dir>", "Cache directory")
+        .action(runClear);
+    program
+        .command("schema")
+        .description("Export JSON Schema for a cached tool's parameters")
+        .argument("<tool_id>", "Tool ID")
+        .option("--version <ver>", "Tool version")
+        .option("--representation <rep>", "State representation (e.g., workflow_step)", "workflow_step")
+        .option("--output <file>", "Output file (default: stdout)")
+        .option("--cache-dir <dir>", "Cache directory")
+        .action(runSchema);
+    program
+        .command("populate-workflow")
+        .description("Scan a workflow and cache all referenced tools")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .option("--cache-dir <dir>", "Cache directory")
+        .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
+        .action(runPopulateWorkflow);
+    program
+        .command("structural-schema")
+        .description("Export the structural JSON Schema for Galaxy workflows")
+        .option("--format <fmt>", "Workflow format: format2 (default) or native", "format2")
+        .option("--output <file>", "Output file (default: stdout)")
+        .action(runStructuralSchema);
+    return program;
+}
+//# sourceMappingURL=galaxy-tool-cache.js.map

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

@@ -0,0 +1 @@
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package/dist/programs/gxwf.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare function buildGxwfProgram(): Command;
+//# sourceMappingURL=gxwf.d.ts.map

package/dist/programs/gxwf.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoBpC,wBAAgB,gBAAgB,IAAI,OAAO,CAsQ1C"}

package/dist/programs/gxwf.js

@@ -0,0 +1,204 @@
+import { Command } from "commander";
+import { runClean } from "../commands/clean.js";
+import { runCleanTree } from "../commands/clean-tree.js";
+import { runConvert } from "../commands/convert.js";
+import { runConvertTree } from "../commands/convert-tree.js";
+import { runRoundtrip } from "../commands/roundtrip.js";
+import { runRoundtripTree } from "../commands/roundtrip-tree.js";
+import { runLint } from "../commands/lint.js";
+import { runMermaid } from "../commands/mermaid.js";
+import { runLintTree } from "../commands/lint-tree.js";
+import { runValidateWorkflow } from "../commands/validate-workflow.js";
+import { runValidateTests } from "../commands/validate-tests.js";
+import { runValidateTestsTree } from "../commands/validate-tests-tree.js";
+import { runValidateTree } from "../commands/validate-tree.js";
+import { runToolSearch } from "../commands/tool-search.js";
+import { runToolVersions } from "../commands/tool-versions.js";
+import { runToolRevisions } from "../commands/tool-revisions.js";
+import { runRepoSearch } from "../commands/repo-search.js";
+import { addStrictOptions } from "../commands/strict-options.js";
+export function buildGxwfProgram() {
+    const program = new Command();
+    program
+        .name("gxwf")
+        .description("Galaxy workflow operations — validate, clean, lint, convert (single-file and tree)")
+        .version("1.0.0");
+    addStrictOptions(program
+        .command("validate")
+        .description("Validate Galaxy workflow files (structure + optional tool state)")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--no-tool-state", "Skip tool state validation")
+        .option("--cache-dir <dir>", "Tool cache directory")
+        .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
+        .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
+        .option("--json", "Output structured JSON report")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateWorkflow);
+    program
+        .command("validate-tests")
+        .description("Validate a workflow-test file (*-tests.yml, *.gxwf-tests.yml) against the Galaxy Tests schema")
+        .argument("<file>", "Tests file (*-tests.yml)")
+        .option("--json", "Output structured JSON report")
+        .option("--workflow <path>", "Cross-check job inputs + output assertions against a workflow (.ga / .gxwf.yml)")
+        .action(runValidateTests);
+    program
+        .command("clean")
+        .description("Strip stale keys and decode legacy tool_state encoding")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .option("--output <file>", "Write cleaned workflow to file (default: stdout)")
+        .option("--diff", "Show diff of changes instead of writing output")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--json", "Output structured JSON report")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
+        .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
+        .action(runClean);
+    addStrictOptions(program
+        .command("lint")
+        .description("Lint Galaxy workflow — structural checks, best practices, tool state validation")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
+        .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
+        .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--json", "Output structured JSON result")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLint);
+    addStrictOptions(program
+        .command("convert")
+        .description("Convert between native (.ga) and format2 (.gxwf.yml) formats")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
+        .option("--output <file>", "Write result to file (default: stdout)")
+        .option("--compact", "Omit position info in format2 output")
+        .option("--json", "Force JSON output")
+        .option("--yaml", "Force YAML output")
+        .option("--format <fmt>", "Force source format (auto-detected by default)")
+        .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
+        .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvert);
+    addStrictOptions(program
+        .command("roundtrip")
+        .description("Roundtrip-validate a native workflow: native → format2 → native, diff tool_state")
+        .argument("<file>", "Native workflow file (.ga)")
+        .option("--cache-dir <dir>", "Tool cache directory")
+        .option("--format <fmt>", "Force source format (must resolve to native)")
+        .option("--json", "Output structured JSON report")
+        .option("--errors-only", "Suppress benign diffs and clean steps from output")
+        .option("--benign-only", "Show only steps with benign diffs (no errors, no failures)")
+        .option("--brief", "Omit per-diff list; show only the one-line summary")).action(runRoundtrip);
+    program
+        .command("mermaid")
+        .description("Render a Galaxy workflow as a Mermaid flowchart diagram")
+        .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+        .argument("[output]", "Output path (.mmd for raw, .md for fenced code block); stdout if omitted")
+        .option("--comments", "Render frame comments as Mermaid subgraphs")
+        .action((file, output, opts) => runMermaid(file, { output, comments: opts.comments }));
+    // -- Tree (batch) variants --
+    addStrictOptions(program
+        .command("validate-tree")
+        .description("Batch validate all workflows under a directory")
+        .argument("<dir>", "Directory to scan for workflows")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--no-tool-state", "Skip tool state validation")
+        .option("--cache-dir <dir>", "Tool cache directory")
+        .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
+        .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
+        .option("--json", "Output structured JSON report")
+        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runValidateTree);
+    addStrictOptions(program
+        .command("lint-tree")
+        .description("Batch lint all workflows under a directory")
+        .argument("<dir>", "Directory to scan for workflows")
+        .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
+        .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
+        .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--json", "Output structured JSON report")
+        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runLintTree);
+    program
+        .command("clean-tree")
+        .description("Batch clean all workflows under a directory")
+        .argument("<dir>", "Directory to scan for workflows")
+        .option("--output-dir <dir>", "Write cleaned workflows to directory (mirrors source tree)")
+        .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+        .option("--json", "Output structured JSON report")
+        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")
+        .option("--skip-uuid", "Skip stripping uuid fields (errors are always stripped)")
+        .action(runCleanTree);
+    addStrictOptions(program
+        .command("convert-tree")
+        .description("Batch convert all workflows under a directory")
+        .argument("<dir>", "Directory to scan for workflows")
+        .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
+        .option("--output-dir <dir>", "Write converted workflows to directory (required)")
+        .option("--compact", "Omit position info in format2 output")
+        .option("--report-json", "Output structured JSON report")
+        .option("--json", "Force JSON output for converted files")
+        .option("--yaml", "Force YAML output")
+        .option("--format <fmt>", "Force source format (auto-detected by default)")
+        .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
+        .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")).action(runConvertTree);
+    addStrictOptions(program
+        .command("roundtrip-tree")
+        .description("Batch roundtrip-validate native workflows under a directory")
+        .argument("<dir>", "Directory to scan for native workflows")
+        .option("--cache-dir <dir>", "Tool cache directory")
+        .option("--format <fmt>", "Force source format (must resolve to native)")
+        .option("--json", "Output structured JSON report")
+        .option("--errors-only", "List only files with errors or failures")
+        .option("--benign-only", "List only files with benign diffs (no errors, no failures)")
+        .option("--brief", "Omit per-file lines; print only the aggregate summary")
+        .option("--report-markdown [file]", "Write Markdown report to file (or stdout if omitted)")
+        .option("--report-html [file]", "Write HTML report to file (or stdout if omitted)")).action(runRoundtripTree);
+    program
+        .command("validate-tests-tree")
+        .description("Batch validate workflow-test files (*-tests.yml / *.gxwf-tests.yml) under a directory")
+        .argument("<dir>", "Directory to scan for test files")
+        .option("--json", "Output structured JSON report")
+        .option("--auto-workflow", "Pair each tests file with a sibling workflow by filename convention (foo.gxwf-tests.yml ↔ foo.gxwf.yml/foo.ga) and cross-check inputs/outputs")
+        .action(runValidateTestsTree);
+    program
+        .command("tool-search")
+        .description("Search the Galaxy Tool Shed for tools matching a query")
+        .argument("<query>", "Search text (e.g. 'fastqc')")
+        .option("--page-size <n>", "Server-side page size", "20")
+        .option("--max-results <n>", "Hard cap on hits returned", "50")
+        .option("--page <n>", "Starting page (1-indexed)", "1")
+        .option("--owner <user>", "Filter hits to a single repo owner (client-side)")
+        .option("--match-name", "Drop hits where the query is not a token in the tool name")
+        .option("--json", "Emit machine-readable JSON envelope")
+        .option("--enrich", "Resolve each hit's ParsedTool and attach it as `parsedTool` (one fetch per hit; off by default)")
+        .option("--cache-dir <dir>", "Tool cache directory (used by --enrich; shared with galaxy-tool-cache)")
+        .action(runToolSearch);
+    program
+        .command("tool-versions")
+        .description("List TRS-published versions of a Tool Shed tool (newest last)")
+        .argument("<tool-id>", "TRS id (owner~repo~tool_id) or pretty form (owner/repo/tool_id)")
+        .option("--json", "Emit machine-readable JSON envelope")
+        .option("--latest", "Print only the latest version")
+        .action(runToolVersions);
+    program
+        .command("tool-revisions")
+        .description("List changeset revisions that publish a Tool Shed tool (ordered oldest→newest). " +
+        "Use for reproducible (name, owner, changeset_revision) workflow pins. " +
+        "Caveat: version strings are not monotonic — the same version can appear in multiple changesets.")
+        .argument("<tool-id>", "TRS id (owner~repo~tool_id) or pretty form (owner/repo/tool_id)")
+        .option("--tool-version <v>", "Restrict to revisions that publish this exact tool version")
+        .option("--latest", "Print only the newest matching revision")
+        .option("--json", "Emit machine-readable JSON envelope")
+        .action(runToolRevisions);
+    program
+        .command("repo-search")
+        .description("Search the Galaxy Tool Shed for repositories. Ranking is popularity-boosted; supports server-side --owner / --category filters via reserved keywords.")
+        .argument("<query>", "Search text (e.g. 'fastqc')")
+        .option("--page-size <n>", "Server-side page size", "20")
+        .option("--max-results <n>", "Hard cap on hits returned", "50")
+        .option("--page <n>", "Starting page (1-indexed)", "1")
+        .option("--owner <user>", "Restrict to a single owner (server-side `owner:` keyword)")
+        .option("--category <name>", "Restrict to a category (server-side `category:` keyword)")
+        .option("--json", "Emit machine-readable JSON envelope")
+        .action(runRepoSearch);
+    return program;
+}
+//# sourceMappingURL=gxwf.js.map

package/dist/programs/gxwf.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.0.0",
+  "version": "1.1.0",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -34,8 +34,9 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/core": "1.0.0",
-    "@galaxy-tool-util/schema": "1.0.0"
+    "@galaxy-tool-util/core": "1.1.0",
+    "@galaxy-tool-util/schema": "1.1.0",
+    "@galaxy-tool-util/search": "1.1.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",