@galaxy-tool-util/cli 0.1.0 → 0.4.0

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 John Chilton
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

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

@@ -4,7 +4,9 @@ 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")
@@ -46,5 +48,18 @@ program
     .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();
 //# 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,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AAEvE,MAAM,OAAO,GAAG,IAAI,OAAO,EAAE,CAAC;AAE9B,OAAO;KACJ,IAAI,CAAC,mBAAmB,CAAC;KACzB,WAAW,CAAC,wCAAwC,CAAC;KACrD,OAAO,CAAC,OAAO,CAAC,CAAC;AAEpB,OAAO;KACJ,OAAO,CAAC,KAAK,CAAC;KACd,WAAW,CAAC,gDAAgD,CAAC;KAC7D,QAAQ,CAAC,WAAW,EAAE,wCAAwC,CAAC;KAC/D,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,oBAAoB,EAAE,kCAAkC,CAAC;KAChE,MAAM,CAAC,MAAM,CAAC,CAAC;AAElB,OAAO;KACJ,OAAO,CAAC,MAAM,CAAC;KACf,WAAW,CAAC,mBAAmB,CAAC;KAChC,MAAM,CAAC,QAAQ,EAAE,gBAAgB,CAAC;KAClC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,OAAO,CAAC,CAAC;AAEnB,OAAO;KACJ,OAAO,CAAC,MAAM,CAAC;KACf,WAAW,CAAC,iCAAiC,CAAC;KAC9C,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC;KAChC,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,OAAO,CAAC,CAAC;AAEnB,OAAO;KACJ,OAAO,CAAC,OAAO,CAAC;KAChB,WAAW,CAAC,oBAAoB,CAAC;KACjC,QAAQ,CAAC,UAAU,EAAE,uCAAuC,CAAC;KAC7D,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,QAAQ,CAAC,CAAC;AAEpB,OAAO;KACJ,OAAO,CAAC,QAAQ,CAAC;KACjB,WAAW,CAAC,mDAAmD,CAAC;KAChE,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC;KAChC,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,wBAAwB,EAAE,4CAA4C,EAAE,eAAe,CAAC;KAC/F,MAAM,CAAC,iBAAiB,EAAE,+BAA+B,CAAC;KAC1D,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,SAAS,CAAC,CAAC;AAErB,OAAO;KACJ,OAAO,CAAC,mBAAmB,CAAC;KAC5B,WAAW,CAAC,gDAAgD,CAAC;KAC7D,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,oBAAoB,EAAE,kCAAkC,CAAC;KAChE,MAAM,CAAC,mBAAmB,CAAC,CAAC;AAE/B,OAAO;KACJ,OAAO,CAAC,mBAAmB,CAAC;KAC5B,WAAW,CAAC,wDAAwD,CAAC;KACrE,MAAM,CAAC,gBAAgB,EAAE,8CAA8C,EAAE,SAAS,CAAC;KACnF,MAAM,CAAC,iBAAiB,EAAE,+BAA+B,CAAC;KAC1D,MAAM,CAAC,mBAAmB,CAAC,CAAC;AAE/B,OAAO,CAAC,KAAK,EAAE,CAAC"}

package/dist/bin/gxwf.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=gxwf.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/bin/gxwf.ts"],"names":[],"mappings":""}

package/dist/bin/gxwf.js

@@ -0,0 +1,150 @@
+#!/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 { 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);
+// -- 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();
+//# sourceMappingURL=gxwf.js.map

package/dist/bin/gxwf.js.map

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

@@ -1,6 +1,6 @@
-import { ToolInfoService } from "@galaxy-tool-util/core";
+import { makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
 export async function runAdd(toolId, opts) {
-    const service = new ToolInfoService({
+    const service = makeNodeToolInfoService({
         cacheDir: opts.cacheDir,
         galaxyUrl: opts.galaxyUrl,
     });

package/dist/commands/add.js.map

@@ -1 +1 @@
-{"version":3,"file":"add.js","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AAQzD,MAAM,CAAC,KAAK,UAAU,MAAM,CAAC,MAAc,EAAE,IAAgB;IAC3D,MAAM,OAAO,GAAG,IAAI,eAAe,CAAC;QAClC,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,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"}

package/dist/commands/clean-tree.d.ts

@@ -0,0 +1,9 @@
+import { type ReportOutputOptions } from "./report-output.js";
+export interface CleanTreeOptions extends ReportOutputOptions {
+    outputDir?: string;
+    format?: string;
+    json?: boolean;
+    skipUuid?: boolean;
+}
+export declare function runCleanTree(dir: string, opts: CleanTreeOptions): Promise<void>;
+//# sourceMappingURL=clean-tree.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean-tree.d.ts","sourceRoot":"","sources":["../../src/commands/clean-tree.ts"],"names":[],"mappings":"AAeA,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,gBAAiB,SAAQ,mBAAmB;IAC3D,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED,wBAAsB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAmDrF"}

package/dist/commands/clean-tree.js

@@ -0,0 +1,69 @@
+/**
+ * `gxwf clean-tree` — batch clean all workflows under a directory.
+ */
+import { cleanWorkflow, buildWorkflowCleanResult, buildTreeCleanReport, } from "@galaxy-tool-util/schema";
+import { mkdir, writeFile } from "node:fs/promises";
+import { dirname, join } from "node:path";
+import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
+import { collectTree } from "./tree.js";
+import { writeReportOutput, writeReportHtml } from "./report-output.js";
+export async function runCleanTree(dir, opts) {
+    const outputDir = opts.outputDir;
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const format = resolveFormat(data, opts.format);
+        const cleanOpts = { skipUuid: opts.skipUuid };
+        const { results: stepResults } = await cleanWorkflow(data, cleanOpts);
+        if (outputDir) {
+            const outPath = join(outputDir, info.relativePath);
+            await mkdir(dirname(outPath), { recursive: true });
+            const serialized = serializeWorkflow(data, format);
+            await writeFile(outPath, serialized, "utf-8");
+        }
+        return buildWorkflowCleanResult(info.relativePath, stepResults);
+    });
+    const report = buildReport(treeResult);
+    await writeReportOutput("clean_tree.md.j2", report, { reportMarkdown: opts.reportMarkdown });
+    await writeReportHtml("clean-tree", report, opts.reportHtml);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = report.summary.affected > 0 ? 1 : 0;
+        return;
+    }
+    // Text output
+    for (const wf of report.workflows) {
+        if (wf.error) {
+            console.error(`  ${wf.path}: ERROR (${wf.error})`);
+            continue;
+        }
+        if (wf.skipped_reason) {
+            console.warn(`  ${wf.path}: SKIPPED (${wf.skipped_reason})`);
+            continue;
+        }
+        const changed = wf.total_removed > 0;
+        console.log(`  ${wf.path}: ${changed ? "CHANGED" : "clean"}`);
+    }
+    const s = report.summary;
+    const total = report.workflows.length;
+    const suffix = outputDir ? ` (written to ${outputDir})` : "";
+    console.log(`\nSummary: ${total} workflows | ${s.affected} changed, ${s.clean} unchanged${suffix}`);
+    // Exit 1 if any workflows had stale keys (like Python's clean-tree)
+    process.exitCode = s.affected > 0 ? 1 : 0;
+}
+function buildReport(treeResult) {
+    const workflows = [];
+    for (const o of treeResult.outcomes) {
+        if (o.error) {
+            workflows.push(buildWorkflowCleanResult(o.info.relativePath, [], { error: o.error }));
+            continue;
+        }
+        if (o.skipped) {
+            workflows.push(buildWorkflowCleanResult(o.info.relativePath, [], {
+                skipped_reason: o.skipReason ?? null,
+            }));
+            continue;
+        }
+        workflows.push(o.result);
+    }
+    return buildTreeCleanReport(treeResult.root, workflows);
+}
+//# sourceMappingURL=clean-tree.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean-tree.js","sourceRoot":"","sources":["../../src/commands/clean-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EACL,aAAa,EAIb,wBAAwB,EACxB,oBAAoB,GACrB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AACpE,OAAO,EAAE,WAAW,EAAmB,MAAM,WAAW,CAAC;AACzD,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAA4B,MAAM,oBAAoB,CAAC;AASlG,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,GAAW,EAAE,IAAsB;IACpE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC;IAEjC,MAAM,UAAU,GAAG,MAAM,WAAW,CAAsB,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QAClF,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,SAAS,GAAyB,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACpE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,aAAa,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;QAEtE,IAAI,SAAS,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,YAAY,CAAC,CAAC;YACnD,MAAM,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;YACnD,MAAM,UAAU,GAAG,iBAAiB,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;YACnD,MAAM,SAAS,CAAC,OAAO,EAAE,UAAU,EAAE,OAAO,CAAC,CAAC;QAChD,CAAC;QAED,OAAO,wBAAwB,CAAC,IAAI,CAAC,YAAY,EAAE,WAAW,CAAC,CAAC;IAClE,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,WAAW,CAAC,UAAU,CAAC,CAAC;IAEvC,MAAM,iBAAiB,CAAC,kBAAkB,EAAE,MAAM,EAAE,EAAE,cAAc,EAAE,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IAC7F,MAAM,eAAe,CAAC,YAAY,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAE7D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,MAAM,CAAC,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACvD,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QAClC,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC;YACnD,SAAS;QACX,CAAC;QACD,IAAI,EAAE,CAAC,cAAc,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC,cAAc,GAAG,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QACD,MAAM,OAAO,GAAG,EAAE,CAAC,aAAa,GAAG,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;IAChE,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IACtC,MAAM,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,SAAS,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;IAC7D,OAAO,CAAC,GAAG,CACT,cAAc,KAAK,gBAAgB,CAAC,CAAC,QAAQ,aAAa,CAAC,CAAC,KAAK,aAAa,MAAM,EAAE,CACvF,CAAC;IACF,oEAAoE;IACpE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC5C,CAAC;AAED,SAAS,WAAW,CAAC,UAA2C;IAC9D,MAAM,SAAS,GAA0B,EAAE,CAAC;IAE5C,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,SAAS,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;YACtF,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,SAAS,CAAC,IAAI,CACZ,wBAAwB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,EAAE;gBAChD,cAAc,EAAG,CAAC,CAAC,UAAgC,IAAI,IAAI;aAC5D,CAAC,CACH,CAAC;YACF,SAAS;QACX,CAAC;QACD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,MAAO,CAAC,CAAC;IAC5B,CAAC;IAED,OAAO,oBAAoB,CAAC,UAAU,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;AAC1D,CAAC"}

package/dist/commands/clean.d.ts

@@ -0,0 +1,10 @@
+export interface CleanOptions {
+    output?: string;
+    diff?: boolean;
+    format?: string;
+    json?: boolean;
+    reportHtml?: string | boolean;
+    skipUuid?: boolean;
+}
+export declare function runClean(filePath: string, opts: CleanOptions): Promise<void>;
+//# sourceMappingURL=clean.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean.d.ts","sourceRoot":"","sources":["../../src/commands/clean.ts"],"names":[],"mappings":"AAgBA,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED,wBAAsB,QAAQ,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CA0ClF"}

package/dist/commands/clean.js

@@ -0,0 +1,48 @@
+/**
+ * `gxwf clean` — strip stale keys and decode legacy tool_state encoding.
+ */
+import { cleanWorkflow, buildSingleCleanReport, } from "@galaxy-tool-util/schema";
+import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
+import { writeReportHtml } from "./report-output.js";
+export async function runClean(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const format = resolveFormat(data, opts.format);
+    const before = opts.diff ? JSON.stringify(data, null, 2) : null;
+    const cleanOpts = { skipUuid: opts.skipUuid };
+    const { results } = await cleanWorkflow(data, cleanOpts);
+    if (opts.json || opts.reportHtml) {
+        const report = buildSingleCleanReport(filePath, results);
+        if (opts.json) {
+            console.log(JSON.stringify(report, null, 2));
+        }
+        await writeReportHtml("clean", report, opts.reportHtml);
+        return;
+    }
+    if (opts.diff) {
+        const after = JSON.stringify(data, null, 2);
+        if (before === after) {
+            console.log("No changes.");
+            return;
+        }
+        // Simple line-by-line diff
+        const beforeLines = before.split("\n");
+        const afterLines = after.split("\n");
+        const maxLen = Math.max(beforeLines.length, afterLines.length);
+        for (let i = 0; i < maxLen; i++) {
+            const bLine = beforeLines[i];
+            const aLine = afterLines[i];
+            if (bLine !== aLine) {
+                if (bLine !== undefined)
+                    console.log(`- ${bLine}`);
+                if (aLine !== undefined)
+                    console.log(`+ ${aLine}`);
+            }
+        }
+        return;
+    }
+    const output = serializeWorkflow(data, format);
+    await writeWorkflowOutput(output, opts.output, "Cleaned workflow");
+}
+//# sourceMappingURL=clean.js.map

package/dist/commands/clean.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"clean.js","sourceRoot":"","sources":["../../src/commands/clean.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EACL,aAAa,EACb,sBAAsB,GAEvB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,gBAAgB,EAChB,aAAa,EACb,iBAAiB,EACjB,mBAAmB,GACpB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAWrD,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,QAAgB,EAAE,IAAkB;IACjE,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;IAChD,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAEhE,MAAM,SAAS,GAAyB,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC;IACpE,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,aAAa,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;IAEzD,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;QACjC,MAAM,MAAM,GAAG,sBAAsB,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QACzD,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC/C,CAAC;QACD,MAAM,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;QACxD,OAAO;IACT,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;QAC5C,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;YACrB,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;YAC3B,OAAO;QACT,CAAC;QACD,2BAA2B;QAC3B,MAAM,WAAW,GAAG,MAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACrC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC,CAAC;QAC/D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAChC,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;YAC7B,MAAM,KAAK,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;YAC5B,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;gBACpB,IAAI,KAAK,KAAK,SAAS;oBAAE,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,EAAE,CAAC,CAAC;gBACnD,IAAI,KAAK,KAAK,SAAS;oBAAE,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,EAAE,CAAC,CAAC;YACrD,CAAC;QACH,CAAC;QACD,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,iBAAiB,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IAC/C,MAAM,mBAAmB,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,kBAAkB,CAAC,CAAC;AACrE,CAAC"}

package/dist/commands/clear.js

@@ -1,10 +1,10 @@
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 export async function runClear(prefix, opts) {
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    const before = cache.listCached().length;
+    const before = (await cache.listCached()).length;
     await cache.clearCache(prefix);
-    const after = cache.listCached().length;
+    const after = (await cache.listCached()).length;
     const removed = before - after;
     if (prefix) {
         console.log(`Removed ${removed} entries matching "${prefix}".`);

package/dist/commands/clear.js.map

@@ -1 +1 @@
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+{"version":3,"file":"clear.js","sourceRoot":"","sources":["../../src/commands/clear.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAMhE,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,MAA0B,EAAE,IAAkB;IAC3E,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,CAAC,MAAM,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC;IACjD,MAAM,KAAK,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC;IAC/B,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC;IAChD,MAAM,OAAO,GAAG,MAAM,GAAG,KAAK,CAAC;IAC/B,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,CAAC,GAAG,CAAC,WAAW,OAAO,sBAAsB,MAAM,IAAI,CAAC,CAAC;IAClE,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,GAAG,CAAC,WAAW,OAAO,sBAAsB,CAAC,CAAC;IACxD,CAAC;AACH,CAAC"}

package/dist/commands/convert-tree.d.ts

@@ -0,0 +1,32 @@
+import { type StepConversionStatus } from "@galaxy-tool-util/schema";
+import { type ToolLoadStatus } from "./stateful-tool-inputs.js";
+import { type StrictOptions } from "./strict-options.js";
+import { type TreeSummary } from "./tree.js";
+export interface ConvertTreeOptions extends StrictOptions {
+    to?: string;
+    outputDir?: string;
+    compact?: boolean;
+    yaml?: boolean;
+    format?: string;
+    json?: boolean;
+    reportJson?: boolean;
+    stateful?: boolean;
+    cacheDir?: string;
+}
+export interface WorkflowConvertResult {
+    relativePath: string;
+    sourceFormat: string;
+    targetFormat: string;
+    statefulSteps?: StepConversionStatus[];
+    toolLoadErrors?: ToolLoadStatus[];
+}
+export interface ConvertTreeReport {
+    root: string;
+    results: (WorkflowConvertResult | {
+        relativePath: string;
+        error: string;
+    })[];
+    summary: TreeSummary;
+}
+export declare function runConvertTree(dir: string, opts: ConvertTreeOptions): Promise<void>;
+//# sourceMappingURL=convert-tree.d.ts.map

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

@@ -0,0 +1 @@
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