@galaxy-tool-util/cli 0.2.0 → 1.0.0

package/dist/bin/gxwf.js

@@ -7,15 +7,19 @@ 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");
-program
+addStrictOptions(program
     .command("validate")
     .description("Validate Galaxy workflow files (structure + optional tool state)")
     .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
@@ -24,7 +28,15 @@ program
     .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)")
-    .action(runValidateWorkflow);
+    .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")
@@ -32,8 +44,11 @@ program
     .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);
-program
+addStrictOptions(program
     .command("lint")
     .description("Lint Galaxy workflow — structural checks, best practices, tool state validation")
     .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
@@ -42,8 +57,8 @@ program
     .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")
-    .action(runLint);
-program
+    .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)")
@@ -54,9 +69,8 @@ program
     .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);
-program
+    .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)")
@@ -65,10 +79,16 @@ program
     .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 --
+    .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")
@@ -78,8 +98,9 @@ program
     .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")
-    .action(runValidateTree);
-program
+    .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")
@@ -88,7 +109,8 @@ program
     .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")
-    .action(runLintTree);
+    .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")
@@ -96,8 +118,11 @@ program
     .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);
-program
+addStrictOptions(program
     .command("convert-tree")
     .description("Batch convert all workflows under a directory")
     .argument("<dir>", "Directory to scan for workflows")
@@ -109,9 +134,8 @@ program
     .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);
-program
+    .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")
@@ -121,6 +145,14 @@ program
     .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")
-    .action(runRoundtripTree);
+    .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

@@ -1 +1 @@
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+{"version":3,"file":"gxwf.js","sourceRoot":"","sources":["../../src/bin/gxwf.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AACzD,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAC;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,oBAAoB,EAAE,MAAM,oCAAoC,CAAC;AAC1E,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE,MAAM,OAAO,GAAG,IAAI,OAAO,EAAE,CAAC;AAE9B,OAAO;KACJ,IAAI,CAAC,MAAM,CAAC;KACZ,WAAW,CAAC,oFAAoF,CAAC;KACjG,OAAO,CAAC,OAAO,CAAC,CAAC;AAEpB,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,UAAU,CAAC;KACnB,WAAW,CAAC,kEAAkE,CAAC;KAC/E,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,iBAAiB,EAAE,4BAA4B,CAAC;KACvD,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,CAAC;KACnD,MAAM,CAAC,eAAe,EAAE,qDAAqD,EAAE,QAAQ,CAAC;KACxF,MAAM,CACL,yBAAyB,EACzB,gFAAgF,CACjF;KACA,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC,CACtF,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;AAE9B,OAAO;KACJ,OAAO,CAAC,gBAAgB,CAAC;KACzB,WAAW,CACV,+FAA+F,CAChG;KACA,QAAQ,CAAC,QAAQ,EAAE,0BAA0B,CAAC;KAC9C,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CACL,mBAAmB,EACnB,iFAAiF,CAClF;KACA,MAAM,CAAC,gBAAgB,CAAC,CAAC;AAE5B,OAAO;KACJ,OAAO,CAAC,OAAO,CAAC;KAChB,WAAW,CAAC,wDAAwD,CAAC;KACrE,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,iBAAiB,EAAE,kDAAkD,CAAC;KAC7E,MAAM,CAAC,QAAQ,EAAE,gDAAgD,CAAC;KAClE,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC;KAClF,MAAM,CAAC,aAAa,EAAE,yDAAyD,CAAC;KAChF,MAAM,CAAC,QAAQ,CAAC,CAAC;AAEpB,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,MAAM,CAAC;KACf,WAAW,CAAC,iFAAiF,CAAC;KAC9F,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,uBAAuB,EAAE,8CAA8C,CAAC;KAC/E,MAAM,CAAC,yBAAyB,EAAE,4DAA4D,CAAC;KAC/F,MAAM,CAAC,mBAAmB,EAAE,6CAA6C,CAAC;KAC1E,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC,CACtF,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;AAElB,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,SAAS,CAAC;KAClB,WAAW,CAAC,8DAA8D,CAAC;KAC3E,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,eAAe,EAAE,+DAA+D,CAAC;KACxF,MAAM,CAAC,iBAAiB,EAAE,wCAAwC,CAAC;KACnE,MAAM,CAAC,WAAW,EAAE,sCAAsC,CAAC;KAC3D,MAAM,CAAC,QAAQ,EAAE,mBAAmB,CAAC;KACrC,MAAM,CAAC,QAAQ,EAAE,mBAAmB,CAAC;KACrC,MAAM,CAAC,gBAAgB,EAAE,gDAAgD,CAAC;KAC1E,MAAM,CAAC,YAAY,EAAE,gEAAgE,CAAC;KACtF,MAAM,CAAC,mBAAmB,EAAE,uCAAuC,CAAC,CACxE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;AAErB,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,WAAW,CAAC;KACpB,WAAW,CAAC,kFAAkF,CAAC;KAC/F,QAAQ,CAAC,QAAQ,EAAE,4BAA4B,CAAC;KAChD,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,CAAC;KACnD,MAAM,CAAC,gBAAgB,EAAE,8CAA8C,CAAC;KACxE,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,eAAe,EAAE,mDAAmD,CAAC;KAC5E,MAAM,CAAC,eAAe,EAAE,4DAA4D,CAAC;KACrF,MAAM,CAAC,SAAS,EAAE,oDAAoD,CAAC,CAC3E,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC;AAEvB,OAAO;KACJ,OAAO,CAAC,SAAS,CAAC;KAClB,WAAW,CAAC,yDAAyD,CAAC;KACtE,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,QAAQ,CAAC,UAAU,EAAE,0EAA0E,CAAC;KAChG,MAAM,CAAC,YAAY,EAAE,4CAA4C,CAAC;KAClE,MAAM,CAAC,CAAC,IAAY,EAAE,MAA0B,EAAE,IAA4B,EAAE,EAAE,CACjF,UAAU,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CACtD,CAAC;AAEJ,8BAA8B;AAE9B,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,eAAe,CAAC;KACxB,WAAW,CAAC,gDAAgD,CAAC;KAC7D,QAAQ,CAAC,OAAO,EAAE,iCAAiC,CAAC;KACpD,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,iBAAiB,EAAE,4BAA4B,CAAC;KACvD,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,CAAC;KACnD,MAAM,CAAC,eAAe,EAAE,qDAAqD,EAAE,QAAQ,CAAC;KACxF,MAAM,CACL,yBAAyB,EACzB,gFAAgF,CACjF;KACA,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,0BAA0B,EAAE,sDAAsD,CAAC;KAC1F,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC,CACtF,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;AAE1B,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,WAAW,CAAC;KACpB,WAAW,CAAC,4CAA4C,CAAC;KACzD,QAAQ,CAAC,OAAO,EAAE,iCAAiC,CAAC;KACpD,MAAM,CAAC,uBAAuB,EAAE,8CAA8C,CAAC;KAC/E,MAAM,CAAC,yBAAyB,EAAE,4DAA4D,CAAC;KAC/F,MAAM,CAAC,mBAAmB,EAAE,6CAA6C,CAAC;KAC1E,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,0BAA0B,EAAE,sDAAsD,CAAC;KAC1F,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC,CACtF,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;AAEtB,OAAO;KACJ,OAAO,CAAC,YAAY,CAAC;KACrB,WAAW,CAAC,6CAA6C,CAAC;KAC1D,QAAQ,CAAC,OAAO,EAAE,iCAAiC,CAAC;KACpD,MAAM,CAAC,oBAAoB,EAAE,4DAA4D,CAAC;KAC1F,MAAM,CAAC,gBAAgB,EAAE,4DAA4D,CAAC;KACtF,MAAM,CAAC,QAAQ,EAAE,+BAA+B,CAAC;KACjD,MAAM,CAAC,0BAA0B,EAAE,sDAAsD,CAAC;KAC1F,MAAM,CAAC,sBAAsB,EAAE,kDAAkD,CAAC;KAClF,MAAM,CAAC,aAAa,EAAE,yDAAyD,CAAC;KAChF,MAAM,CAAC,YAAY,CAAC,CAAC;AAExB,gBAAgB,CACd,OAAO;KACJ,OAAO,CAAC,cAAc,CAAC;KACvB,WAAW,CAAC,+CAA+C,CAAC;KAC5D,QAAQ,CAAC,OAAO,EAAE,iCAAiC,CAAC;KACpD,MAAM,CAAC,eAAe,EAAE,+DAA+D,CAAC;KACxF,MAAM,CAAC,oBAAoB,EAAE,mDAAmD,CAAC;KACjF,MAAM,CAAC,WAAW,EAAE,sCAAsC,CAAC;KAC3D,MAAM,CAAC,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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

@@ -1,23 +1,9 @@
-import { type TreeSummary } from "./tree.js";
-export interface CleanTreeOptions {
+import { type ReportOutputOptions } from "./report-output.js";
+export interface CleanTreeOptions extends ReportOutputOptions {
     outputDir?: string;
     format?: string;
     json?: boolean;
-}
-export interface WorkflowCleanResult {
-    relativePath: string;
-    changed: boolean;
-}
-export interface CleanTreeReport {
-    root: string;
-    results: (WorkflowCleanResult | {
-        relativePath: string;
-        error: string;
-    })[];
-    summary: TreeSummary & {
-        changed: number;
-        unchanged: number;
-    };
+    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

@@ -1 +1 @@
-{"version":3,"file":"clean-tree.d.ts","sourceRoot":"","sources":["../../src/commands/clean-tree.ts"],"names":[],"mappings":"AAOA,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,mBAAmB;IAClC,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,mBAAmB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC3E,OAAO,EAAE,WAAW,GAAG;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,CAAC;CAC/D;AAED,wBAAsB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4CrF"}
+{"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

@@ -1,68 +1,69 @@
 /**
  * `gxwf clean-tree` — batch clean all workflows under a directory.
  */
-import { cleanWorkflow } from "@galaxy-tool-util/schema";
+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, summarizeOutcomes } from "./tree.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 before = JSON.stringify(data);
-        cleanWorkflow(data);
-        const changed = JSON.stringify(data) !== before;
+        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 { relativePath: info.relativePath, changed };
+        return buildWorkflowCleanResult(info.relativePath, stepResults);
     });
-    const report = buildCleanReport(treeResult);
+    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.changed > 0 ? 1 : 0;
+        process.exitCode = report.summary.affected > 0 ? 1 : 0;
         return;
     }
     // Text output
-    for (const outcome of treeResult.outcomes) {
-        if (outcome.error) {
-            console.error(`  ${outcome.info.relativePath}: ERROR (${outcome.error})`);
+    for (const wf of report.workflows) {
+        if (wf.error) {
+            console.error(`  ${wf.path}: ERROR (${wf.error})`);
             continue;
         }
-        const r = outcome.result;
-        console.log(`  ${r.relativePath}: ${r.changed ? "CHANGED" : "clean"}`);
+        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: ${s.total} workflows | ${s.changed} changed, ${s.unchanged} unchanged${suffix}`);
+    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.changed > 0 ? 1 : 0;
+    process.exitCode = s.affected > 0 ? 1 : 0;
 }
-function buildCleanReport(treeResult) {
-    const results = [];
-    let changed = 0;
-    let unchanged = 0;
+function buildReport(treeResult) {
+    const workflows = [];
     for (const o of treeResult.outcomes) {
         if (o.error) {
-            results.push({ relativePath: o.info.relativePath, error: o.error });
+            workflows.push(buildWorkflowCleanResult(o.info.relativePath, [], { error: o.error }));
             continue;
         }
         if (o.skipped) {
-            results.push({ relativePath: o.info.relativePath, error: `SKIPPED: ${o.skipReason}` });
+            workflows.push(buildWorkflowCleanResult(o.info.relativePath, [], {
+                skipped_reason: o.skipReason ?? null,
+            }));
             continue;
         }
-        const r = o.result;
-        results.push(r);
-        if (r.changed)
-            changed++;
-        else
-            unchanged++;
+        workflows.push(o.result);
     }
-    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.changed);
-    return { root: treeResult.root, results, summary: { ...wfSummary, changed, unchanged } };
+    return buildTreeCleanReport(treeResult.root, workflows);
 }
 //# sourceMappingURL=clean-tree.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"clean-tree.js","sourceRoot":"","sources":["../../src/commands/clean-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,aAAa,EAAE,MAAM,0BAA0B,CAAC;AACzD,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,EAAE,iBAAiB,EAAqC,MAAM,WAAW,CAAC;AAmB9F,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,GAAW,EAAE,IAAsB;IACpE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC;IAEjC,MAAM,UAAU,GAAG,MAAM,WAAW,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QAC7D,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;QACpC,aAAa,CAAC,IAAI,CAAC,CAAC;QACpB,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,MAAM,CAAC;QAEhD,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,EAAE,YAAY,EAAE,IAAI,CAAC,YAAY,EAAE,OAAO,EAAgC,CAAC;IACpF,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;IAE5C,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,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACtD,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,OAAO,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QAC1C,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,YAAY,YAAY,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC;YAC1E,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,OAAO,CAAC,MAAO,CAAC;QAC1B,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;IACzE,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,SAAS,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;IAC7D,OAAO,CAAC,GAAG,CACT,cAAc,CAAC,CAAC,KAAK,gBAAgB,CAAC,CAAC,OAAO,aAAa,CAAC,CAAC,SAAS,aAAa,MAAM,EAAE,CAC5F,CAAC;IACF,oEAAoE;IACpE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAA2C;IACnE,MAAM,OAAO,GAA+B,EAAE,CAAC;IAC/C,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,OAAO,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACpE,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,OAAO,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,KAAK,EAAE,YAAY,CAAC,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;YACvF,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,CAAC,CAAC,MAAO,CAAC;QACpB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,IAAI,CAAC,CAAC,OAAO;YAAE,OAAO,EAAE,CAAC;;YACpB,SAAS,EAAE,CAAC;IACnB,CAAC;IAED,MAAM,SAAS,GAAG,iBAAiB,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;IAC3E,OAAO,EAAE,IAAI,EAAE,UAAU,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,GAAG,SAAS,EAAE,OAAO,EAAE,SAAS,EAAE,EAAE,CAAC;AAC3F,CAAC"}
+{"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

@@ -2,6 +2,9 @@ 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

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

@@ -1,15 +1,25 @@
 /**
  * `gxwf clean` — strip stale keys and decode legacy tool_state encoding.
  */
-import { cleanWorkflow } from "@galaxy-tool-util/schema";
+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;
-    cleanWorkflow(data);
+    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) {

package/dist/commands/clean.js.map

@@ -1 +1 @@
-{"version":3,"file":"clean.js","sourceRoot":"","sources":["../../src/commands/clean.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,aAAa,EAAE,MAAM,0BAA0B,CAAC;AACzD,OAAO,EACL,gBAAgB,EAChB,aAAa,EACb,iBAAiB,EACjB,mBAAmB,GACpB,MAAM,kBAAkB,CAAC;AAQ1B,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,aAAa,CAAC,IAAI,CAAC,CAAC;IAEpB,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"}
+{"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 @@
-{"version":3,"file":"clear.js","sourceRoot":"","sources":["../../src/commands/clear.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAMnD,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,MAA0B,EAAE,IAAkB;IAC3E,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,KAAK,CAAC,UAAU,EAAE,CAAC,MAAM,CAAC;IACzC,MAAM,KAAK,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC;IAC/B,MAAM,KAAK,GAAG,KAAK,CAAC,UAAU,EAAE,CAAC,MAAM,CAAC;IACxC,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"}
+{"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

@@ -1,7 +1,8 @@
 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 {
+export interface ConvertTreeOptions extends StrictOptions {
     to?: string;
     outputDir?: string;
     compact?: boolean;

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

@@ -1 +1 @@
-{"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"AAIA,OAAO,EAML,KAAK,oBAAoB,EAE1B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EAA6B,KAAK,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAG3F,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,kBAAkB;IACjC,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACvC,cAAc,CAAC,EAAE,cAAc,EAAE,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,qBAAqB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC7E,OAAO,EAAE,WAAW,CAAC;CACtB;AAED,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CA0JzF"}
+{"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"AAKA,OAAO,EAQL,KAAK,oBAAoB,EAE1B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EAA6B,KAAK,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAE3F,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAE/E,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACvC,cAAc,CAAC,EAAE,cAAc,EAAE,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,qBAAqB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC7E,OAAO,EAAE,WAAW,CAAC;CACtB;AAED,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CA+KzF"}

package/dist/commands/convert-tree.js

@@ -1,12 +1,10 @@
-/**
- * `gxwf convert-tree` — batch convert all workflows under a directory.
- */
-import { ToolCache } from "@galaxy-tool-util/core";
-import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
 import { mkdir, writeFile } from "node:fs/promises";
 import { dirname, join, basename } from "node:path";
 import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
 import { collectTree, summarizeOutcomes } from "./tree.js";
 export async function runConvertTree(dir, opts) {
@@ -19,15 +17,29 @@ export async function runConvertTree(dir, opts) {
     // Shared tool cache for stateful mode (loaded once per run)
     let cache = null;
     if (opts.stateful) {
-        cache = new ToolCache({ cacheDir: opts.cacheDir });
+        cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
         await cache.index.load();
-        if (cache.index.listAll().length === 0) {
+        if ((await cache.index.listAll()).length === 0) {
             console.warn("Tool cache is empty — stateful conversion will fall back for every step");
         }
     }
+    const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
         const sourceFormat = resolveFormat(data, opts.format);
         const targetFormat = resolveTargetFormat(sourceFormat, opts.to);
+        // Per-file strict checks on input
+        if (strict.strictEncoding) {
+            const encErrors = checkStrictEncoding(data, sourceFormat);
+            if (encErrors.length > 0) {
+                throw new Error(`Encoding: ${encErrors.join("; ")}`);
+            }
+        }
+        if (strict.strictStructure) {
+            const structErrors = checkStrictStructure(data, sourceFormat);
+            if (structErrors.length > 0) {
+                throw new Error(`Structure: ${structErrors.join("; ")}`);
+            }
+        }
         if (sourceFormat === targetFormat) {
             return {
                 relativePath: info.relativePath,
@@ -79,6 +91,10 @@ export async function runConvertTree(dir, opts) {
         const outPath = join(outputDir, outName);
         await mkdir(dirname(outPath), { recursive: true });
         await writeFile(outPath, serialized, "utf-8");
+        // --strict-state: require all stateful steps to convert successfully
+        if (strict.strictState && statefulSteps?.some((s) => !s.converted)) {
+            throw new Error("Strict state: all steps must convert successfully");
+        }
         return {
             relativePath: info.relativePath,
             sourceFormat,

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

@@ -1 +1 @@
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package/dist/commands/convert.d.ts

@@ -1,4 +1,5 @@
-export interface ConvertOptions {
+import { type StrictOptions } from "./strict-options.js";
+export interface ConvertOptions extends StrictOptions {
     to?: string;
     output?: string;
     compact?: boolean;

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

@@ -1 +1 @@
-{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAuBA,MAAM,WAAW,cAAc;IAC7B,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAoEtF"}
+{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAkBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,MAAM,WAAW,cAAe,SAAQ,aAAa;IACnD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAkGtF"}