@galaxy-tool-util/cli 1.3.0 → 1.5.0

package/dist/commands/_draft-extract.d.ts

@@ -0,0 +1,7 @@
+export interface DraftExtractOptions {
+    output?: string;
+    reportJson?: string | boolean;
+    format?: string;
+}
+export declare function runDraftExtract(filePath: string, opts: DraftExtractOptions): Promise<void>;
+//# sourceMappingURL=_draft-extract.d.ts.map

package/dist/commands/_draft-extract.d.ts.map

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

@@ -0,0 +1,75 @@
+/**
+ * `gxwf _draft-extract` — extract the concrete subset of a draft workflow.
+ *
+ * Hidden agent-loop command: runs `extractConcreteSubset` from
+ * @galaxy-tool-util/schema, strips `_plan_*` planning fields, and promotes
+ * `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any
+ * (sub)workflow that is now fully concrete. Emits the trimmed workflow to
+ * stdout (or `-o` file) and an optional sidecar JSON report.
+ *
+ * Exit codes:
+ *   0 — input parses + extract ran (including empty-extract case)
+ *   2 — parse/read failure, native input rejected, or stdout-sink collision
+ *       (workflow → stdout AND --report-json → stdout simultaneously)
+ */
+import { writeFile } from "node:fs/promises";
+import { buildSingleDraftExtractReport, extractConcreteSubset, promoteFullyConcreteDrafts, resolveFormat, serializeWorkflow, stripPlanFields, } from "@galaxy-tool-util/schema";
+import { readWorkflowFile, writeWorkflowOutput } from "./workflow-io.js";
+import { findStdoutSinkCollision, targetsStdout } from "./report-output.js";
+export async function runDraftExtract(filePath, opts) {
+    const collision = findStdoutSinkCollision([
+        { flag: "<workflow output>", toStdout: !opts.output },
+        { flag: "--report-json", toStdout: targetsStdout(opts.reportJson) },
+    ]);
+    if (collision) {
+        console.error(collision);
+        process.exitCode = 2;
+        return;
+    }
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("_draft-extract requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    const extract = extractConcreteSubset(data);
+    stripPlanFields(extract.workflow);
+    const promote = promoteFullyConcreteDrafts(extract.workflow);
+    const trimmed = extract.workflow != null && typeof extract.workflow === "object"
+        ? extract.workflow
+        : {};
+    const classAfter = trimmed.class === "GalaxyWorkflow" ? "GalaxyWorkflow" : "GalaxyWorkflowDraft";
+    const outputFormat = outputFormatFor(opts.output, format);
+    const serialized = serializeWorkflow(trimmed, outputFormat);
+    await writeWorkflowOutput(serialized, opts.output, "Extracted workflow");
+    if (opts.reportJson !== undefined) {
+        const report = buildSingleDraftExtractReport(filePath, opts.output ?? null, extract, promote, classAfter);
+        const json = JSON.stringify(report, null, 2);
+        const dest = opts.reportJson;
+        if (dest === true || dest === "-") {
+            console.log(json);
+        }
+        else {
+            await writeFile(dest, json + "\n", "utf-8");
+        }
+    }
+    process.exitCode = 0;
+}
+/**
+ * Resolve the workflow serialization format from -o's extension, falling
+ * back to the detected input format. `.ga` / `.json` → native (JSON);
+ * `.gxwf.yml` / other → format2 (YAML).
+ */
+function outputFormatFor(output, fallback) {
+    if (!output)
+        return fallback;
+    if (output.endsWith(".ga") || output.endsWith(".json"))
+        return "native";
+    return "format2";
+}
+//# sourceMappingURL=_draft-extract.js.map

package/dist/commands/_draft-extract.js.map

@@ -0,0 +1 @@
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package/dist/commands/draft-next-step.d.ts

@@ -0,0 +1,6 @@
+export interface DraftNextStepOptions {
+    format?: string;
+    outputFormat?: "json" | "markdown" | string;
+}
+export declare function runDraftNextStep(filePath: string, opts: DraftNextStepOptions): Promise<void>;
+//# sourceMappingURL=draft-next-step.d.ts.map

package/dist/commands/draft-next-step.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"draft-next-step.d.ts","sourceRoot":"","sources":["../../src/commands/draft-next-step.ts"],"names":[],"mappings":"AAeA,MAAM,WAAW,oBAAoB;IACnC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,GAAG,UAAU,GAAG,MAAM,CAAC;CAC7C;AAED,wBAAsB,gBAAgB,CACpC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,oBAAoB,GACzB,OAAO,CAAC,IAAI,CAAC,CA4Bf"}

package/dist/commands/draft-next-step.js

@@ -0,0 +1,49 @@
+/**
+ * `gxwf draft-next-step` — pick the next step a downstream agent should
+ * work on. Wraps `nextDraftStep` from @galaxy-tool-util/schema.
+ *
+ * Default output is JSON (the agent-loop wire format); `--output-format
+ * markdown` renders a human-glance checklist. Pure pass-through — same
+ * input → byte-identical output.
+ *
+ * Exit codes:
+ *   0 — input parses + is a (possibly non-draft) workflow document
+ *   2 — parse/read failure or format mismatch (native rejected)
+ */
+import { nextDraftStep, resolveFormat } from "@galaxy-tool-util/schema";
+import { readWorkflowFile } from "./workflow-io.js";
+export async function runDraftNextStep(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("draft-next-step requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    const result = nextDraftStep(data);
+    const outputFormat = opts.outputFormat ?? "json";
+    if (outputFormat === "markdown") {
+        process.stdout.write(renderMarkdown(result));
+    }
+    else if (outputFormat === "json") {
+        console.log(JSON.stringify(result, null, 2));
+    }
+    else {
+        console.error(`unknown --output-format: ${outputFormat} (expected json or markdown)`);
+        process.exitCode = 2;
+        return;
+    }
+    process.exitCode = 0;
+}
+function renderMarkdown(result) {
+    if (!result.draft)
+        return "_No remaining draft work._\n";
+    const heading = `## Next step: \`${result.step.join(" / ")}\`\n\n`;
+    const items = result.work.map((w) => `- [ ] ${w}`).join("\n");
+    return heading + items + "\n";
+}
+//# sourceMappingURL=draft-next-step.js.map

package/dist/commands/draft-next-step.js.map

@@ -0,0 +1 @@
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package/dist/commands/draft-validate.d.ts

@@ -0,0 +1,8 @@
+export interface DraftValidateOptions {
+    format?: string;
+    json?: boolean;
+    reportHtml?: string | boolean;
+    reportMarkdown?: string | boolean;
+}
+export declare function runDraftValidate(filePath: string, opts: DraftValidateOptions): Promise<void>;
+//# sourceMappingURL=draft-validate.d.ts.map

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

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

@@ -0,0 +1,75 @@
+/**
+ * `gxwf draft-validate` — validate a draft Galaxy workflow
+ * (class: GalaxyWorkflowDraft).
+ *
+ * Wraps `validateDraft` from @galaxy-tool-util/schema. Single-file only; the
+ * tree variant is deferred to workstream v2.
+ *
+ * Exit codes (per workstream C):
+ *   0 — clean draft (no structure/topology/semantic errors; warnings allowed)
+ *   1 — draft validation errors (topology or semantic errors)
+ *   2 — parse failure, format mismatch, or structural decode failure
+ *       (class !== GalaxyWorkflowDraft, schema decode error)
+ */
+import { buildSingleDraftValidationReport, resolveFormat, validateDraft, } from "@galaxy-tool-util/schema";
+import { readWorkflowFile } from "./workflow-io.js";
+import { findStdoutSinkConflict, writeReportHtml, writeReportOutput } from "./report-output.js";
+export async function runDraftValidate(filePath, opts) {
+    const conflict = findStdoutSinkConflict(opts);
+    if (conflict) {
+        console.error(conflict);
+        process.exitCode = 2;
+        return;
+    }
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("draft-validate requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    const result = validateDraft(data);
+    const report = buildSingleDraftValidationReport(filePath, result);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else {
+        printTextReport(report, result);
+    }
+    await writeReportOutput("draft_validate.md.j2", report, opts);
+    await writeReportHtml("draft-validate", report, opts.reportHtml);
+    process.exitCode = exitCodeFor(result);
+}
+function exitCodeFor(result) {
+    if (result.structureErrors.length > 0)
+        return 2;
+    if (result.topologyErrors.length > 0 || result.semanticErrors.length > 0)
+        return 1;
+    return 0;
+}
+function printTextReport(report, result) {
+    console.log(`Draft validation: ${report.workflow}`);
+    console.log(`  ${report.summary}`);
+    printBucket("Structure errors", result.structureErrors);
+    printBucket("Topology errors", result.topologyErrors);
+    printBucket("Semantic errors", result.semanticErrors);
+    printBucket("Warnings", result.warnings);
+    const survey = report.survey;
+    console.log(`  Survey: ${survey.todo_count} TODO sentinel${survey.todo_count === 1 ? "" : "s"}` +
+        ` across ${survey.todo_paths.length} step path${survey.todo_paths.length === 1 ? "" : "s"};` +
+        ` ${survey.plan_step_paths.length} step${survey.plan_step_paths.length === 1 ? "" : "s"} with _plan_* fields`);
+}
+function printBucket(label, diagnostics) {
+    if (diagnostics.length === 0)
+        return;
+    console.log(`  ${label} (${diagnostics.length}):`);
+    for (const d of diagnostics) {
+        const where = d.path.length === 0 ? "<workflow>" : d.path.join("/");
+        console.log(`    ${where}: ${d.message}`);
+    }
+}
+//# sourceMappingURL=draft-validate.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"draft-validate.js","sourceRoot":"","sources":["../../src/commands/draft-validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AACH,OAAO,EACL,gCAAgC,EAChC,aAAa,EACb,aAAa,GAId,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,sBAAsB,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAShG,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,QAAgB,EAChB,IAA0B;IAE1B,MAAM,QAAQ,GAAG,sBAAsB,CAAC,IAAI,CAAC,CAAC;IAC9C,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;QACxB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;IAChD,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,OAAO,CAAC,KAAK,CAAC,qEAAqE,CAAC,CAAC;QACrF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC;IACnC,MAAM,MAAM,GAAG,gCAAgC,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAElE,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;SAAM,CAAC;QACN,eAAe,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,CAAC;IAED,MAAM,iBAAiB,CAAC,sBAAsB,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IAC9D,MAAM,eAAe,CAAC,gBAAgB,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAEjE,OAAO,CAAC,QAAQ,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;AACzC,CAAC;AAED,SAAS,WAAW,CAAC,MAA6B;IAChD,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IAChD,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACnF,OAAO,CAAC,CAAC;AACX,CAAC;AAED,SAAS,eAAe,CAAC,MAAmC,EAAE,MAA6B;IACzF,OAAO,CAAC,GAAG,CAAC,qBAAqB,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC;IACpD,OAAO,CAAC,GAAG,CAAC,KAAK,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC;IACnC,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,eAAe,CAAC,CAAC;IACxD,WAAW,CAAC,iBAAiB,EAAE,MAAM,CAAC,cAAc,CAAC,CAAC;IACtD,WAAW,CAAC,iBAAiB,EAAE,MAAM,CAAC,cAAc,CAAC,CAAC;IACtD,WAAW,CAAC,UAAU,EAAE,MAAM,CAAC,QAAQ,CAAC,CAAC;IACzC,MAAM,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC;IAC7B,OAAO,CAAC,GAAG,CACT,aAAa,MAAM,CAAC,UAAU,iBAAiB,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE;QACjF,WAAW,MAAM,CAAC,UAAU,CAAC,MAAM,aAAa,MAAM,CAAC,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG;QAC5F,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,QAAQ,MAAM,CAAC,eAAe,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,sBAAsB,CAChH,CAAC;AACJ,CAAC;AAED,SAAS,WAAW,CAAC,KAAa,EAAE,WAAwC;IAC1E,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO;IACrC,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,KAAK,WAAW,CAAC,MAAM,IAAI,CAAC,CAAC;IACnD,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;QAC5B,MAAM,KAAK,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACpE,OAAO,CAAC,GAAG,CAAC,OAAO,KAAK,KAAK,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;IAC5C,CAAC;AACH,CAAC"}

package/dist/commands/report-output.d.ts

@@ -1,4 +1,4 @@
-export type ReportType = "validate" | "lint" | "clean" | "validate-tree" | "lint-tree" | "clean-tree" | "roundtrip-tree";
+export type ReportType = "validate" | "lint" | "clean" | "draft-validate" | "validate-tree" | "lint-tree" | "clean-tree" | "roundtrip-tree";
 export interface ReportOutputOptions {
     /**
      * Path to write Markdown report to. Commander sets this to `true` (boolean)
@@ -9,6 +9,32 @@ export interface ReportOutputOptions {
     /** Same semantics as reportMarkdown but for HTML output. */
     reportHtml?: string | boolean;
 }
+/** True if dest is unset to a filename and would write to stdout. */
+declare function targetsStdout(dest: string | boolean | undefined): boolean;
+/**
+ * If more than one sink in `candidates` would write to stdout, return an
+ * error message naming the conflicting flags. Otherwise null.
+ *
+ * Generalizes `findStdoutSinkConflict` for commands whose stdout sinks
+ * aren't drawn from the standard `--json` / `--report-{html,markdown}`
+ * set (e.g. `draft-extract` writes the trimmed workflow to stdout by
+ * default + `--report-json` may also target stdout).
+ */
+export declare function findStdoutSinkCollision(candidates: Array<{
+    flag: string;
+    toStdout: boolean;
+}>): string | null;
+/**
+ * If more than one report sink (JSON + rendered reports) would write to
+ * stdout, return an error message describing the conflict. Otherwise null.
+ */
+export declare function findStdoutSinkConflict(opts: {
+    json?: boolean;
+    reportHtml?: string | boolean;
+    reportMarkdown?: string | boolean;
+}): string | null;
+/** Re-export for command handlers that need their own collision-detection sites. */
+export { targetsStdout };
 /**
  * Render and write report output if --report-markdown / --report-html flags
  * were passed. Both can be specified simultaneously.

package/dist/commands/report-output.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"report-output.d.ts","sourceRoot":"","sources":["../../src/commands/report-output.ts"],"names":[],"mappings":"AAWA,MAAM,MAAM,UAAU,GAClB,UAAU,GACV,MAAM,GACN,OAAO,GACP,eAAe,GACf,WAAW,GACX,YAAY,GACZ,gBAAgB,CAAC;AAErB,MAAM,WAAW,mBAAmB;IAClC;;;;OAIG;IACH,cAAc,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAClC,4DAA4D;IAC5D,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC/B;AAED;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,OAAO,EACf,IAAI,EAAE,mBAAmB,GACxB,OAAO,CAAC,IAAI,CAAC,CAUf;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,SAAgB,GAAG,MAAM,CAgB9F;AAED;;;GAGG;AACH,wBAAsB,eAAe,CACnC,IAAI,EAAE,UAAU,EAChB,IAAI,EAAE,OAAO,EACb,IAAI,EAAE,MAAM,GAAG,OAAO,GAAG,SAAS,EAClC,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,IAAI,CAAC,CAQf"}
+{"version":3,"file":"report-output.d.ts","sourceRoot":"","sources":["../../src/commands/report-output.ts"],"names":[],"mappings":"AAWA,MAAM,MAAM,UAAU,GAClB,UAAU,GACV,MAAM,GACN,OAAO,GACP,gBAAgB,GAChB,eAAe,GACf,WAAW,GACX,YAAY,GACZ,gBAAgB,CAAC;AAErB,MAAM,WAAW,mBAAmB;IAClC;;;;OAIG;IACH,cAAc,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAClC,4DAA4D;IAC5D,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC/B;AAED,qEAAqE;AACrE,iBAAS,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,GAAG,SAAS,GAAG,OAAO,CAElE;AAED;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CACrC,UAAU,EAAE,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,OAAO,CAAA;CAAE,CAAC,GACrD,MAAM,GAAG,IAAI,CAIf;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE;IAC3C,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC9B,cAAc,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CACnC,GAAG,MAAM,GAAG,IAAI,CAMhB;AAED,oFAAoF;AACpF,OAAO,EAAE,aAAa,EAAE,CAAC;AAEzB;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,OAAO,EACf,IAAI,EAAE,mBAAmB,GACxB,OAAO,CAAC,IAAI,CAAC,CAUf;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,SAAgB,GAAG,MAAM,CAgB9F;AAED;;;GAGG;AACH,wBAAsB,eAAe,CACnC,IAAI,EAAE,UAAU,EAChB,IAAI,EAAE,OAAO,EACb,IAAI,EAAE,MAAM,GAAG,OAAO,GAAG,SAAS,EAClC,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,IAAI,CAAC,CAQf"}

package/dist/commands/report-output.js

@@ -7,6 +7,38 @@ import { renderReport } from "../workflow/report-templates.js";
 // Bump when a new shell version with user-visible changes is released to npm.
 const SHELL_CDN_VERSION = "0.1.0";
 const SHELL_CDN_BASE = `https://cdn.jsdelivr.net/npm/@galaxy-tool-util/gxwf-report-shell@${SHELL_CDN_VERSION}/dist`;
+/** True if dest is unset to a filename and would write to stdout. */
+function targetsStdout(dest) {
+    return dest === true || dest === "-";
+}
+/**
+ * If more than one sink in `candidates` would write to stdout, return an
+ * error message naming the conflicting flags. Otherwise null.
+ *
+ * Generalizes `findStdoutSinkConflict` for commands whose stdout sinks
+ * aren't drawn from the standard `--json` / `--report-{html,markdown}`
+ * set (e.g. `draft-extract` writes the trimmed workflow to stdout by
+ * default + `--report-json` may also target stdout).
+ */
+export function findStdoutSinkCollision(candidates) {
+    const sinks = candidates.filter((c) => c.toStdout).map((c) => c.flag);
+    if (sinks.length < 2)
+        return null;
+    return `cannot write ${sinks.join(" + ")} to stdout simultaneously — pick one, or redirect a report to a file`;
+}
+/**
+ * If more than one report sink (JSON + rendered reports) would write to
+ * stdout, return an error message describing the conflict. Otherwise null.
+ */
+export function findStdoutSinkConflict(opts) {
+    return findStdoutSinkCollision([
+        { flag: "--json", toStdout: !!opts.json },
+        { flag: "--report-html", toStdout: targetsStdout(opts.reportHtml) },
+        { flag: "--report-markdown", toStdout: targetsStdout(opts.reportMarkdown) },
+    ]);
+}
+/** Re-export for command handlers that need their own collision-detection sites. */
+export { targetsStdout };
 /**
  * Render and write report output if --report-markdown / --report-html flags
  * were passed. Both can be specified simultaneously.

package/dist/commands/report-output.js.map

@@ -1 +1 @@
-{"version":3,"file":"report-output.js","sourceRoot":"","sources":["../../src/commands/report-output.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,iCAAiC,CAAC;AAE/D,yDAAyD;AACzD,8EAA8E;AAC9E,MAAM,iBAAiB,GAAG,OAAO,CAAC;AAClC,MAAM,cAAc,GAAG,oEAAoE,iBAAiB,OAAO,CAAC;AAsBpH;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,YAAoB,EACpB,MAAe,EACf,IAAyB;IAEzB,MAAM,IAAI,GAAG,IAAI,CAAC,cAAc,CAAC;IACjC,IAAI,CAAC,IAAI;QAAE,OAAO;IAClB,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC;IACzD,6EAA6E;IAC7E,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;QAClC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;SAAM,CAAC;QACN,MAAM,SAAS,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IAC1C,CAAC;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,IAAgB,EAAE,IAAa,EAAE,KAAK,GAAG,aAAa;IACpF,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;IAC/C,OAAO;;;;;WAKE,KAAK;iCACiB,cAAc;;;;qCAIV,OAAO;iBAC3B,cAAc;;QAEvB,CAAC;AACT,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,IAAgB,EAChB,IAAa,EACb,IAAkC,EAClC,KAAc;IAEd,IAAI,CAAC,IAAI;QAAE,OAAO;IAClB,MAAM,OAAO,GAAG,eAAe,CAAC,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC;IACnD,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;QAClC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;SAAM,CAAC;QACN,MAAM,SAAS,CAAC,IAAc,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IACpD,CAAC;AACH,CAAC"}
+{"version":3,"file":"report-output.js","sourceRoot":"","sources":["../../src/commands/report-output.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,iCAAiC,CAAC;AAE/D,yDAAyD;AACzD,8EAA8E;AAC9E,MAAM,iBAAiB,GAAG,OAAO,CAAC;AAClC,MAAM,cAAc,GAAG,oEAAoE,iBAAiB,OAAO,CAAC;AAuBpH,qEAAqE;AACrE,SAAS,aAAa,CAAC,IAAkC;IACvD,OAAO,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,CAAC;AACvC,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,uBAAuB,CACrC,UAAsD;IAEtD,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IACtE,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,IAAI,CAAC;IAClC,OAAO,gBAAgB,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,sEAAsE,CAAC;AACjH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,sBAAsB,CAAC,IAItC;IACC,OAAO,uBAAuB,CAAC;QAC7B,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE;QACzC,EAAE,IAAI,EAAE,eAAe,EAAE,QAAQ,EAAE,aAAa,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE;QACnE,EAAE,IAAI,EAAE,mBAAmB,EAAE,QAAQ,EAAE,aAAa,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE;KAC5E,CAAC,CAAC;AACL,CAAC;AAED,oFAAoF;AACpF,OAAO,EAAE,aAAa,EAAE,CAAC;AAEzB;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,YAAoB,EACpB,MAAe,EACf,IAAyB;IAEzB,MAAM,IAAI,GAAG,IAAI,CAAC,cAAc,CAAC;IACjC,IAAI,CAAC,IAAI;QAAE,OAAO;IAClB,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC;IACzD,6EAA6E;IAC7E,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;QAClC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;SAAM,CAAC;QACN,MAAM,SAAS,CAAC,IAAI,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IAC1C,CAAC;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,IAAgB,EAAE,IAAa,EAAE,KAAK,GAAG,aAAa;IACpF,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;IAC/C,OAAO;;;;;WAKE,KAAK;iCACiB,cAAc;;;;qCAIV,OAAO;iBAC3B,cAAc;;QAEvB,CAAC;AACT,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,IAAgB,EAChB,IAAa,EACb,IAAkC,EAClC,KAAc;IAEd,IAAI,CAAC,IAAI;QAAE,OAAO;IAClB,MAAM,OAAO,GAAG,eAAe,CAAC,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC;IACnD,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;QAClC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;SAAM,CAAC;QACN,MAAM,SAAS,CAAC,IAAc,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC;IACpD,CAAC;AACH,CAAC"}

package/dist/commands/structural-schema.js

@@ -1,5 +1,5 @@
 /**
- * `galaxy-tool-cache structural-schema` — export the structural JSON Schema
+ * `gxwf structural-schema` — export the structural JSON Schema
  * for Galaxy workflow validation (gxformat2 or native).
  */
 import { GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema } from "@galaxy-tool-util/schema";

package/dist/commands/validate-tool-source-tree.d.ts

@@ -0,0 +1,28 @@
+/**
+ * ``gxwf validate-tool-source-tree`` — batch-validate every user-defined tool
+ * source YAML under a directory. Discovery parses each candidate YAML and
+ * checks for ``class: GalaxyUserTool`` / ``class: GalaxyTool`` rather than
+ * relying on a filename suffix (UDTs don't have an established convention).
+ */
+import { type UserToolSourceDiagnostic } from "@galaxy-tool-util/schema";
+export interface ValidateToolSourceTreeOptions {
+    json?: boolean;
+    schemaOnly?: boolean;
+}
+export interface ToolSourceTreeFileReport {
+    path: string;
+    valid: boolean;
+    errors: UserToolSourceDiagnostic[];
+}
+export interface ValidateToolSourceTreeReport {
+    root: string;
+    files: ToolSourceTreeFileReport[];
+    summary: {
+        total: number;
+        ok: number;
+        fail: number;
+        error: number;
+    };
+}
+export declare function runValidateToolSourceTree(dir: string, opts?: ValidateToolSourceTreeOptions): Promise<void>;
+//# sourceMappingURL=validate-tool-source-tree.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"validate-tool-source-tree.d.ts","sourceRoot":"","sources":["../../src/commands/validate-tool-source-tree.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAA0B,KAAK,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AAEjG,MAAM,WAAW,6BAA6B;IAC5C,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,wBAAwB;IACvC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,wBAAwB,EAAE,CAAC;CACpC;AAED,MAAM,WAAW,4BAA4B;IAC3C,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,wBAAwB,EAAE,CAAC;IAClC,OAAO,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,EAAE,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CACrE;AAqED,wBAAsB,yBAAyB,CAC7C,GAAG,EAAE,MAAM,EACX,IAAI,GAAE,6BAAkC,GACvC,OAAO,CAAC,IAAI,CAAC,CAyCf"}

package/dist/commands/validate-tool-source-tree.js

@@ -0,0 +1,113 @@
+/**
+ * ``gxwf validate-tool-source-tree`` — batch-validate every user-defined tool
+ * source YAML under a directory. Discovery parses each candidate YAML and
+ * checks for ``class: GalaxyUserTool`` / ``class: GalaxyTool`` rather than
+ * relying on a filename suffix (UDTs don't have an established convention).
+ */
+import { readdir, readFile } from "node:fs/promises";
+import { join, relative } from "node:path";
+import { parse as parseYaml } from "yaml";
+import { validateUserToolSource } from "@galaxy-tool-util/schema";
+const EXCLUDE_DIRS = new Set([".git", ".hg", ".venv", "node_modules", "__pycache__", ".snakemake"]);
+const YAML_EXTS = [".yml", ".yaml"];
+const TOOL_CLASSES = new Set(["GalaxyUserTool", "GalaxyTool"]);
+function isYamlFile(name) {
+    return YAML_EXTS.some((e) => name.endsWith(e));
+}
+async function discoverYamlFiles(root) {
+    const out = [];
+    await walk(root, out);
+    out.sort();
+    return out;
+}
+async function walk(dir, out) {
+    let entries;
+    try {
+        entries = await readdir(dir, { withFileTypes: true });
+    }
+    catch {
+        return;
+    }
+    for (const entry of entries) {
+        if (entry.isDirectory()) {
+            if (!EXCLUDE_DIRS.has(entry.name)) {
+                await walk(join(dir, entry.name), out);
+            }
+            continue;
+        }
+        if (entry.isFile() && isYamlFile(entry.name)) {
+            out.push(join(dir, entry.name));
+        }
+    }
+}
+async function validateOne(path, root, schemaOnly) {
+    const rel = relative(root, path);
+    let parsed;
+    try {
+        const raw = await readFile(path, "utf-8");
+        parsed = parseYaml(raw);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        return {
+            path: rel,
+            valid: false,
+            loadError: true,
+            errors: [
+                { path: "(root)", message: `YAML parse error: ${msg}`, keyword: "yaml", params: {} },
+            ],
+        };
+    }
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+        return undefined;
+    }
+    const cls = parsed["class"];
+    if (typeof cls !== "string" || !TOOL_CLASSES.has(cls)) {
+        return undefined;
+    }
+    const { valid, errors } = validateUserToolSource(parsed, { schemaOnly });
+    return { path: rel, valid, errors };
+}
+export async function runValidateToolSourceTree(dir, opts = {}) {
+    const paths = await discoverYamlFiles(dir);
+    const files = [];
+    for (const p of paths) {
+        const result = await validateOne(p, dir, opts.schemaOnly === true);
+        if (result)
+            files.push(result);
+    }
+    const summary = {
+        total: files.length,
+        ok: files.filter((f) => f.valid).length,
+        fail: files.filter((f) => !f.valid && !f.loadError).length,
+        error: files.filter((f) => f.loadError).length,
+    };
+    const report = {
+        root: dir,
+        files: files.map(({ path, valid, errors }) => ({ path, valid, errors })),
+        summary,
+    };
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else {
+        for (const f of files) {
+            if (f.loadError) {
+                console.error(`  ${f.path}: ERROR (${f.errors[0]?.message ?? "load failed"})`);
+            }
+            else if (f.valid) {
+                console.log(`  ${f.path}: OK`);
+            }
+            else {
+                console.error(`  ${f.path}: ${f.errors.length} validation error(s)`);
+                for (const e of f.errors) {
+                    console.error(`    ${e.path}: ${e.message} [${e.keyword}]`);
+                }
+            }
+        }
+        const s = summary;
+        console.log(`\nSummary: ${s.total} files | ${s.ok} OK, ${s.fail} FAIL, ${s.error} ERROR`);
+    }
+    process.exitCode = summary.fail > 0 || summary.error > 0 ? 1 : 0;
+}
+//# sourceMappingURL=validate-tool-source-tree.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"validate-tool-source-tree.js","sourceRoot":"","sources":["../../src/commands/validate-tool-source-tree.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AACrD,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,KAAK,IAAI,SAAS,EAAE,MAAM,MAAM,CAAC;AAC1C,OAAO,EAAE,sBAAsB,EAAiC,MAAM,0BAA0B,CAAC;AAmBjG,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,cAAc,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC,CAAC;AACpG,MAAM,SAAS,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AACpC,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC,CAAC,gBAAgB,EAAE,YAAY,CAAC,CAAC,CAAC;AAE/D,SAAS,UAAU,CAAC,IAAY;IAC9B,OAAO,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;AACjD,CAAC;AAED,KAAK,UAAU,iBAAiB,CAAC,IAAY;IAC3C,MAAM,GAAG,GAAa,EAAE,CAAC;IACzB,MAAM,IAAI,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;IACtB,GAAG,CAAC,IAAI,EAAE,CAAC;IACX,OAAO,GAAG,CAAC;AACb,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,GAAW,EAAE,GAAa;IAC5C,IAAI,OAAO,CAAC;IACZ,IAAI,CAAC;QACH,OAAO,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACxD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO;IACT,CAAC;IACD,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;YACxB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;gBAClC,MAAM,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,EAAE,GAAG,CAAC,CAAC;YACzC,CAAC;YACD,SAAS;QACX,CAAC;QACD,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;AACH,CAAC;AAED,KAAK,UAAU,WAAW,CACxB,IAAY,EACZ,IAAY,EACZ,UAAmB;IAEnB,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IACjC,IAAI,MAAe,CAAC;IACpB,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;QAC1C,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC;IAC1B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO;YACL,IAAI,EAAE,GAAG;YACT,KAAK,EAAE,KAAK;YACZ,SAAS,EAAE,IAAI;YACf,MAAM,EAAE;gBACN,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,qBAAqB,GAAG,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;aACrF;SACF,CAAC;IACJ,CAAC;IACD,IAAI,CAAC,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;QACnE,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,MAAM,GAAG,GAAI,MAAkC,CAAC,OAAO,CAAC,CAAC;IACzD,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;QACtD,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,sBAAsB,CAAC,MAAM,EAAE,EAAE,UAAU,EAAE,CAAC,CAAC;IACzE,OAAO,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;AACtC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,yBAAyB,CAC7C,GAAW,EACX,OAAsC,EAAE;IAExC,MAAM,KAAK,GAAG,MAAM,iBAAiB,CAAC,GAAG,CAAC,CAAC;IAC3C,MAAM,KAAK,GAA2D,EAAE,CAAC;IACzE,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;QACtB,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,CAAC;QACnE,IAAI,MAAM;YAAE,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACjC,CAAC;IAED,MAAM,OAAO,GAAG;QACd,KAAK,EAAE,KAAK,CAAC,MAAM;QACnB,EAAE,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM;QACvC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,MAAM;QAC1D,KAAK,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,MAAM;KAC/C,CAAC;IAEF,MAAM,MAAM,GAAiC;QAC3C,IAAI,EAAE,GAAG;QACT,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC;QACxE,OAAO;KACR,CAAC;IAEF,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;SAAM,CAAC;QACN,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;YACtB,IAAI,CAAC,CAAC,SAAS,EAAE,CAAC;gBAChB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,IAAI,aAAa,GAAG,CAAC,CAAC;YACjF,CAAC;iBAAM,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;gBACnB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC;YACjC,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,MAAM,CAAC,MAAM,sBAAsB,CAAC,CAAC;gBACrE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;oBACzB,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,OAAO,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC;gBAC9D,CAAC;YACH,CAAC;QACH,CAAC;QACD,MAAM,CAAC,GAAG,OAAO,CAAC;QAClB,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,KAAK,YAAY,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,KAAK,QAAQ,CAAC,CAAC;IAC5F,CAAC;IAED,OAAO,CAAC,QAAQ,GAAG,OAAO,CAAC,IAAI,GAAG,CAAC,IAAI,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AACnE,CAAC"}

package/dist/commands/validate-tool-source.d.ts

@@ -0,0 +1,20 @@
+/**
+ * ``gxwf validate-tool-source`` — validate a user-defined Galaxy tool source
+ * YAML file (``class: GalaxyUserTool`` / ``class: GalaxyTool``) against the
+ * JSON Schema synced from Galaxy's ``galaxy.tool_util_models.DynamicToolSources``
+ * Pydantic models, plus the semantic checks added in
+ * galaxyproject/galaxy#22615 (input refs, output discovery, citation shape,
+ * blank required fields).
+ */
+import { type UserToolSourceDiagnostic } from "@galaxy-tool-util/schema";
+export interface ValidateToolSourceOptions {
+    json?: boolean;
+    schemaOnly?: boolean;
+}
+export interface ValidateToolSourceReport {
+    file: string;
+    valid: boolean;
+    errors: UserToolSourceDiagnostic[];
+}
+export declare function runValidateToolSource(filePath: string, opts?: ValidateToolSourceOptions): Promise<void>;
+//# sourceMappingURL=validate-tool-source.d.ts.map

package/dist/commands/validate-tool-source.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"validate-tool-source.d.ts","sourceRoot":"","sources":["../../src/commands/validate-tool-source.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAA0B,KAAK,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AAEjG,MAAM,WAAW,yBAAyB;IACxC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,wBAAwB;IACvC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,wBAAwB,EAAE,CAAC;CACpC;AAED,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,IAAI,GAAE,yBAA8B,GACnC,OAAO,CAAC,IAAI,CAAC,CAsCf"}

package/dist/commands/validate-tool-source.js

@@ -0,0 +1,52 @@
+/**
+ * ``gxwf validate-tool-source`` — validate a user-defined Galaxy tool source
+ * YAML file (``class: GalaxyUserTool`` / ``class: GalaxyTool``) against the
+ * JSON Schema synced from Galaxy's ``galaxy.tool_util_models.DynamicToolSources``
+ * Pydantic models, plus the semantic checks added in
+ * galaxyproject/galaxy#22615 (input refs, output discovery, citation shape,
+ * blank required fields).
+ */
+import { readFile } from "node:fs/promises";
+import { parse as parseYaml } from "yaml";
+import { validateUserToolSource } from "@galaxy-tool-util/schema";
+export async function runValidateToolSource(filePath, opts = {}) {
+    const raw = await readFile(filePath, "utf-8");
+    let parsed;
+    try {
+        parsed = parseYaml(raw);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        if (opts.json) {
+            const report = {
+                file: filePath,
+                valid: false,
+                errors: [
+                    { path: "(root)", message: `YAML parse error: ${msg}`, keyword: "yaml", params: {} },
+                ],
+            };
+            console.log(JSON.stringify(report, null, 2));
+        }
+        else {
+            console.error(`${filePath}: YAML parse error: ${msg}`);
+        }
+        process.exitCode = 2;
+        return;
+    }
+    const { valid, errors } = validateUserToolSource(parsed, { schemaOnly: opts.schemaOnly });
+    if (opts.json) {
+        const report = { file: filePath, valid, errors };
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else if (valid) {
+        console.log(`${filePath}: OK`);
+    }
+    else {
+        console.error(`${filePath}: ${errors.length} validation error(s)`);
+        for (const e of errors) {
+            console.error(`  ${e.path}: ${e.message} [${e.keyword}]`);
+        }
+    }
+    process.exitCode = valid ? 0 : 1;
+}
+//# sourceMappingURL=validate-tool-source.js.map

package/dist/commands/validate-tool-source.js.map

@@ -0,0 +1 @@
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package/dist/commands/validate-workflow.d.ts.map

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

@@ -8,7 +8,7 @@ import { createDefaultResolver } from "./url-resolver.js";
 import { renderStepResults } from "./render-results.js";
 import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
 import { resolveStrictOptions } from "./strict-options.js";
-import { writeReportHtml } from "./report-output.js";
+import { findStdoutSinkConflict, writeReportHtml } from "./report-output.js";
 import { buildConnectionReport } from "./connection-validation.js";
 function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
@@ -27,6 +27,12 @@ export function decodeStructureErrors(data, format) {
     return [];
 }
 export async function runValidateWorkflow(filePath, opts) {
+    const conflict = findStdoutSinkConflict(opts);
+    if (conflict) {
+        console.error(conflict);
+        process.exitCode = 2;
+        return;
+    }
     const data = await readWorkflowFile(filePath);
     if (!data)
         return;

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

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package/dist/index.d.ts

@@ -22,6 +22,12 @@ export type { ValidateTestsOptions, ValidateTestsReport } from "./commands/valid
 /** Batch-validate workflow-test files under a directory. */
 export { runValidateTestsTree } from "./commands/validate-tests-tree.js";
 export type { ValidateTestsTreeOptions, ValidateTestsTreeReport, } from "./commands/validate-tests-tree.js";
+/** Validate a user-defined Galaxy tool source YAML (class: GalaxyUserTool / GalaxyTool). */
+export { runValidateToolSource } from "./commands/validate-tool-source.js";
+export type { ValidateToolSourceOptions, ValidateToolSourceReport, } from "./commands/validate-tool-source.js";
+/** Batch-validate user-defined Galaxy tool source YAMLs under a directory. */
+export { runValidateToolSourceTree } from "./commands/validate-tool-source-tree.js";
+export type { ValidateToolSourceTreeOptions, ValidateToolSourceTreeReport, } from "./commands/validate-tool-source-tree.js";
 /** Clean a Galaxy workflow — strip stale keys and decode legacy encoding. */
 export { runClean } from "./commands/clean.js";
 /** Lint a Galaxy workflow — structural checks, best practices, tool state validation. */

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,yCAAyC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,0CAA0C;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,4DAA4D;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,2FAA2F;AAC3F,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,yEAAyE;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sEAAsE;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,YAAY,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,8BAA8B,CAAC;AAC9F,4DAA4D;AAC5D,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AACzE,YAAY,EACV,wBAAwB,EACxB,uBAAuB,GACxB,MAAM,mCAAmC,CAAC;AAC3C,6EAA6E;AAC7E,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,yFAAyF;AACzF,OAAO,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACjE,YAAY,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACxE,oEAAoE;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,sDAAsD;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,8DAA8D;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sDAAsD;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,kDAAkD;AAClD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,mDAAmD;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,qDAAqD;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,wCAAwC;AACxC,OAAO,EACL,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EACjB,YAAY,EACZ,gBAAgB,GACjB,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjG,iDAAiD;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACjE,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChE,4EAA4E;AAC5E,OAAO,EACL,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,iCAAiC,CAAC;AACzC,kFAAkF;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAC/E,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAC;AAC3F,wEAAwE;AACxE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,gEAAgE;AAChE,OAAO,EACL,sBAAsB,EACtB,+BAA+B,EAC/B,uCAAuC,GACxC,MAAM,oCAAoC,CAAC;AAC5C,YAAY,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAC;AAC3E,6EAA6E;AAC7E,OAAO,EACL,6BAA6B,EAC7B,8BAA8B,EAC9B,+BAA+B,GAChC,MAAM,6CAA6C,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,yCAAyC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,0CAA0C;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,4DAA4D;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,2FAA2F;AAC3F,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,yEAAyE;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sEAAsE;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,YAAY,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,8BAA8B,CAAC;AAC9F,4DAA4D;AAC5D,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AACzE,YAAY,EACV,wBAAwB,EACxB,uBAAuB,GACxB,MAAM,mCAAmC,CAAC;AAC3C,4FAA4F;AAC5F,OAAO,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAC;AAC3E,YAAY,EACV,yBAAyB,EACzB,wBAAwB,GACzB,MAAM,oCAAoC,CAAC;AAC5C,8EAA8E;AAC9E,OAAO,EAAE,yBAAyB,EAAE,MAAM,yCAAyC,CAAC;AACpF,YAAY,EACV,6BAA6B,EAC7B,4BAA4B,GAC7B,MAAM,yCAAyC,CAAC;AACjD,6EAA6E;AAC7E,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,yFAAyF;AACzF,OAAO,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACjE,YAAY,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACxE,oEAAoE;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,sDAAsD;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,8DAA8D;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sDAAsD;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,kDAAkD;AAClD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,mDAAmD;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,qDAAqD;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,wCAAwC;AACxC,OAAO,EACL,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EACjB,YAAY,EACZ,gBAAgB,GACjB,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjG,iDAAiD;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACjE,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChE,4EAA4E;AAC5E,OAAO,EACL,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,iCAAiC,CAAC;AACzC,kFAAkF;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAC/E,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAC;AAC3F,wEAAwE;AACxE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,gEAAgE;AAChE,OAAO,EACL,sBAAsB,EACtB,+BAA+B,EAC/B,uCAAuC,GACxC,MAAM,oCAAoC,CAAC;AAC5C,YAAY,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAC;AAC3E,6EAA6E;AAC7E,OAAO,EACL,6BAA6B,EAC7B,8BAA8B,EAC9B,+BAA+B,GAChC,MAAM,6CAA6C,CAAC"}

package/dist/index.js

@@ -20,6 +20,10 @@ export { runValidateWorkflow } from "./commands/validate-workflow.js";
 export { runValidateTests } from "./commands/validate-tests.js";
 /** Batch-validate workflow-test files under a directory. */
 export { runValidateTestsTree } from "./commands/validate-tests-tree.js";
+/** Validate a user-defined Galaxy tool source YAML (class: GalaxyUserTool / GalaxyTool). */
+export { runValidateToolSource } from "./commands/validate-tool-source.js";
+/** Batch-validate user-defined Galaxy tool source YAMLs under a directory. */
+export { runValidateToolSourceTree } from "./commands/validate-tool-source-tree.js";
 /** Clean a Galaxy workflow — strip stale keys and decode legacy encoding. */
 export { runClean } from "./commands/clean.js";
 /** Lint a Galaxy workflow — structural checks, best practices, tool state validation. */

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,yCAAyC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,0CAA0C;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,4DAA4D;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,2FAA2F;AAC3F,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,yEAAyE;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sEAAsE;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAEhE,4DAA4D;AAC5D,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AAKzE,6EAA6E;AAC7E,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,yFAAyF;AACzF,OAAO,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAEjE,oEAAoE;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,sDAAsD;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,8DAA8D;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sDAAsD;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,kDAAkD;AAClD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,mDAAmD;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,qDAAqD;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,wCAAwC;AACxC,OAAO,EACL,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EACjB,YAAY,EACZ,gBAAgB,GACjB,MAAM,oBAAoB,CAAC;AAE5B,iDAAiD;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACjE,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChE,4EAA4E;AAC5E,OAAO,EACL,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,iCAAiC,CAAC;AACzC,kFAAkF;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAE/E,wEAAwE;AACxE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,gEAAgE;AAChE,OAAO,EACL,sBAAsB,EACtB,+BAA+B,EAC/B,uCAAuC,GACxC,MAAM,oCAAoC,CAAC;AAE5C,6EAA6E;AAC7E,OAAO,EACL,6BAA6B,EAC7B,8BAA8B,EAC9B,+BAA+B,GAChC,MAAM,6CAA6C,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,yCAAyC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,0CAA0C;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,4DAA4D;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,2FAA2F;AAC3F,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,yEAAyE;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sEAAsE;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAEhE,4DAA4D;AAC5D,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AAKzE,4FAA4F;AAC5F,OAAO,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAC;AAK3E,8EAA8E;AAC9E,OAAO,EAAE,yBAAyB,EAAE,MAAM,yCAAyC,CAAC;AAKpF,6EAA6E;AAC7E,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,yFAAyF;AACzF,OAAO,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAEjE,oEAAoE;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,sDAAsD;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,8DAA8D;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sDAAsD;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,kDAAkD;AAClD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,mDAAmD;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,qDAAqD;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,wCAAwC;AACxC,OAAO,EACL,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EACjB,YAAY,EACZ,gBAAgB,GACjB,MAAM,oBAAoB,CAAC;AAE5B,iDAAiD;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACjE,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChE,4EAA4E;AAC5E,OAAO,EACL,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,iCAAiC,CAAC;AACzC,kFAAkF;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAE/E,wEAAwE;AACxE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,gEAAgE;AAChE,OAAO,EACL,sBAAsB,EACtB,+BAA+B,EAC/B,uCAAuC,GACxC,MAAM,oCAAoC,CAAC;AAE5C,6EAA6E;AAC7E,OAAO,EACL,6BAA6B,EAC7B,8BAA8B,EAC9B,+BAA+B,GAChC,MAAM,6CAA6C,CAAC"}

package/dist/meta/spec-types.d.ts

@@ -28,6 +28,8 @@ export interface SpecCommand {
     optionGroups?: string[];
     /** Key into the handler registry passed to `buildProgramFromSpec`. */
     handler: string;
+    /** When true, suppress this command from `--help` output. */
+    hidden?: boolean;
 }
 export interface ProgramSpec {
     name: string;

package/dist/meta/spec-types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"spec-types.d.ts","sourceRoot":"","sources":["../../src/meta/spec-types.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,MAAM,WAAW,UAAU;IACzB,gFAAgF;IAChF,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,iEAAiE;IACjE,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC5B;AAED,MAAM,WAAW,OAAO;IACtB,4EAA4E;IAC5E,GAAG,EAAE,MAAM,CAAC;IACZ,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,EAAE,CAAC;IACjB,OAAO,CAAC,EAAE,UAAU,EAAE,CAAC;IACvB,mFAAmF;IACnF,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,sEAAsE;IACtE,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,mFAAmF;IACnF,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,UAAU,EAAE,CAAC,CAAC;IAC5C,QAAQ,EAAE,WAAW,EAAE,CAAC;CACzB"}
+{"version":3,"file":"spec-types.d.ts","sourceRoot":"","sources":["../../src/meta/spec-types.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,MAAM,WAAW,UAAU;IACzB,gFAAgF;IAChF,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,iEAAiE;IACjE,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;CAC5B;AAED,MAAM,WAAW,OAAO;IACtB,4EAA4E;IAC5E,GAAG,EAAE,MAAM,CAAC;IACZ,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,EAAE,CAAC;IACjB,OAAO,CAAC,EAAE,UAAU,EAAE,CAAC;IACvB,mFAAmF;IACnF,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,sEAAsE;IACtE,OAAO,EAAE,MAAM,CAAC;IAChB,6DAA6D;IAC7D,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,mFAAmF;IACnF,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,UAAU,EAAE,CAAC,CAAC;IAC5C,QAAQ,EAAE,WAAW,EAAE,CAAC;CACzB"}

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

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

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

@@ -5,7 +5,6 @@ import { runClear } from "../commands/clear.js";
 import { runPopulateWorkflow } from "../commands/populate-workflow.js";
 import { runSchema } from "../commands/schema.js";
 import { runSummarize } from "../commands/summarize.js";
-import { runStructuralSchema } from "../commands/structural-schema.js";
 import { buildProgramFromSpec } from "../spec/build-program.js";
 import { galaxyToolCacheSpec } from "../meta/specs.js";
 const handlers = {
@@ -16,7 +15,6 @@ const handlers = {
     schema: runSchema,
     summarize: runSummarize,
     populateWorkflow: runPopulateWorkflow,
-    structuralSchema: runStructuralSchema,
 };
 export function buildGalaxyToolCacheProgram() {
     return buildProgramFromSpec(galaxyToolCacheSpec, handlers);

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

@@ -1 +1 @@
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+{"version":3,"file":"galaxy-tool-cache.js","sourceRoot":"","sources":["../../src/programs/galaxy-tool-cache.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAwB,MAAM,0BAA0B,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kBAAkB,CAAC;AAEvD,MAAM,QAAQ,GAAoB;IAChC,GAAG,EAAE,MAAM;IACX,IAAI,EAAE,OAAO;IACb,IAAI,EAAE,OAAO;IACb,KAAK,EAAE,QAAQ;IACf,MAAM,EAAE,SAAS;IACjB,SAAS,EAAE,YAAY;IACvB,gBAAgB,EAAE,mBAAmB;CACtC,CAAC;AAEF,MAAM,UAAU,2BAA2B;IACzC,OAAO,oBAAoB,CAAC,mBAAmB,EAAE,QAAQ,CAAC,CAAC;AAC7D,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuEzC,wBAAgB,gBAAgB,IAAI,OAAO,CAE1C"}
+{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAmFzC,wBAAgB,gBAAgB,IAAI,OAAO,CAE1C"}

package/dist/programs/gxwf.js

@@ -1,5 +1,8 @@
 import { runClean } from "../commands/clean.js";
 import { runCleanTree } from "../commands/clean-tree.js";
+import { runDraftExtract } from "../commands/_draft-extract.js";
+import { runDraftNextStep } from "../commands/draft-next-step.js";
+import { runDraftValidate } from "../commands/draft-validate.js";
 import { runConvert } from "../commands/convert.js";
 import { runConvertTree } from "../commands/convert-tree.js";
 import { runRoundtrip } from "../commands/roundtrip.js";
@@ -11,17 +14,23 @@ 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 { runValidateToolSource } from "../commands/validate-tool-source.js";
+import { runValidateToolSourceTree } from "../commands/validate-tool-source-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 { runStructuralSchema } from "../commands/structural-schema.js";
 import { buildProgramFromSpec } from "../spec/build-program.js";
 import { gxwfSpec } from "../meta/specs.js";
 const handlers = {
     validateWorkflow: runValidateWorkflow,
     validateTests: runValidateTests,
     clean: runClean,
+    draftExtract: runDraftExtract,
+    draftNextStep: runDraftNextStep,
+    draftValidate: runDraftValidate,
     lint: runLint,
     convert: runConvert,
     roundtrip: runRoundtrip,
@@ -45,10 +54,13 @@ const handlers = {
     convertTree: runConvertTree,
     roundtripTree: runRoundtripTree,
     validateTestsTree: runValidateTestsTree,
+    validateToolSource: runValidateToolSource,
+    validateToolSourceTree: runValidateToolSourceTree,
     toolSearch: runToolSearch,
     toolVersions: runToolVersions,
     toolRevisions: runToolRevisions,
     repoSearch: runRepoSearch,
+    structuralSchema: runStructuralSchema,
 };
 export function buildGxwfProgram() {
     return buildProgramFromSpec(gxwfSpec, handlers);

package/dist/programs/gxwf.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gxwf.js","sourceRoot":"","sources":["../../src/programs/gxwf.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAChE,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,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,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,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,qBAAqB,EAAE,MAAM,qCAAqC,CAAC;AAC5E,OAAO,EAAE,yBAAyB,EAAE,MAAM,0CAA0C,CAAC;AACrF,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,aAAa,EAAE,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,oBAAoB,EAAwB,MAAM,0BAA0B,CAAC;AACtF,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAE5C,MAAM,QAAQ,GAAoB;IAChC,gBAAgB,EAAE,mBAAmB;IACrC,aAAa,EAAE,gBAAgB;IAC/B,KAAK,EAAE,QAAQ;IACf,YAAY,EAAE,eAAe;IAC7B,aAAa,EAAE,gBAAgB;IAC/B,aAAa,EAAE,gBAAgB;IAC/B,IAAI,EAAE,OAAO;IACb,OAAO,EAAE,UAAU;IACnB,SAAS,EAAE,YAAY;IACvB,OAAO,EAAE,CACP,IAAY,EACZ,MAA0B,EAC1B,IAA8E,EAC9E,EAAE,CACF,UAAU,CAAC,IAAI,EAAE;QACf,MAAM;QACN,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;QAC7C,QAAQ,EAAE,IAAI,CAAC,QAAQ;KACxB,CAAC;IACJ,WAAW,EAAE,CACX,IAAY,EACZ,MAA0B,EAC1B,IAMC,EACD,EAAE,CACF,cAAc,CAAC,IAAI,EAAE;QACnB,MAAM;QACN,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;QAC7C,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,MAAM,EAAE,IAAI,CAAC,MAAM;KACpB,CAAC;IACJ,YAAY,EAAE,eAAe;IAC7B,QAAQ,EAAE,WAAW;IACrB,SAAS,EAAE,YAAY;IACvB,WAAW,EAAE,cAAc;IAC3B,aAAa,EAAE,gBAAgB;IAC/B,iBAAiB,EAAE,oBAAoB;IACvC,kBAAkB,EAAE,qBAAqB;IACzC,sBAAsB,EAAE,yBAAyB;IACjD,UAAU,EAAE,aAAa;IACzB,YAAY,EAAE,eAAe;IAC7B,aAAa,EAAE,gBAAgB;IAC/B,UAAU,EAAE,aAAa;IACzB,gBAAgB,EAAE,mBAAmB;CACtC,CAAC;AAEF,MAAM,UAAU,gBAAgB;IAC9B,OAAO,oBAAoB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;AAClD,CAAC"}

package/dist/spec/build-program.js

@@ -11,7 +11,7 @@ export function buildProgramFromSpec(spec, handlers) {
     program.name(spec.name).description(spec.description).version(spec.version);
     const groups = spec.optionGroups ?? {};
     for (const cmd of spec.commands) {
-        program.addCommand(buildCommand(cmd, groups, handlers));
+        program.addCommand(buildCommand(cmd, groups, handlers), cmd.hidden ? { hidden: true } : {});
     }
     return program;
 }

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

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package/dist/workflow/_templates-bundled.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"_templates-bundled.d.ts","sourceRoot":"","sources":["../../src/workflow/_templates-bundled.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,iBAAiB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAiUpD,CAAC"}
+{"version":3,"file":"_templates-bundled.d.ts","sourceRoot":"","sources":["../../src/workflow/_templates-bundled.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,iBAAiB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAqXpD,CAAC"}

package/dist/workflow/_templates-bundled.js

@@ -142,6 +142,58 @@ All other workflows have no stale keys.
 | - | {{ step_label }} | error | - | {{ err }} |
 {%   endfor %}
 {% endfor %}
+{% endif %}
+`,
+    "draft_validate.md.j2": `{#-
+  Single-file report for \`\`gxwf draft-validate\`\`.
+
+  Context:
+    report — SingleDraftValidationReport from buildSingleDraftValidationReport
+    meta   — optional generated_at / tool_util_version (ignored here)
+-#}
+# Draft Workflow Validation Report
+
+Workflow: \`{{ report.workflow }}\`
+Status: {% if report.ok %}OK{% else %}FAIL{% endif %}
+Summary: {{ report.summary }}
+
+## Survey
+
+- Draft: {% if report.survey.is_draft %}yes{% else %}no{% endif %}
+- TODO sentinels: {{ report.survey.todo_count }} across {{ report.survey.todo_paths | length }} step path(s)
+- Steps with \`_plan_*\` fields: {{ report.survey.plan_step_paths | length }}
+
+{% if report.structure_errors | length > 0 %}
+## Structure Errors ({{ report.structure_errors | length }})
+
+{% for d in report.structure_errors %}
+- \`\`{% if d.path | length == 0 %}<workflow>{% else %}{{ d.path | join("/") }}{% endif %}\`\` — {{ d.message }}
+{% endfor %}
+
+{% endif %}
+{% if report.topology_errors | length > 0 %}
+## Topology Errors ({{ report.topology_errors | length }})
+
+{% for d in report.topology_errors %}
+- \`\`{% if d.path | length == 0 %}<workflow>{% else %}{{ d.path | join("/") }}{% endif %}\`\` — {{ d.message }}
+{% endfor %}
+
+{% endif %}
+{% if report.semantic_errors | length > 0 %}
+## Semantic Errors ({{ report.semantic_errors | length }})
+
+{% for d in report.semantic_errors %}
+- \`\`{% if d.path | length == 0 %}<workflow>{% else %}{{ d.path | join("/") }}{% endif %}\`\` — {{ d.message }}
+{% endfor %}
+
+{% endif %}
+{% if report.warnings | length > 0 %}
+## Warnings ({{ report.warnings | length }})
+
+{% for d in report.warnings %}
+- \`\`{% if d.path | length == 0 %}<workflow>{% else %}{{ d.path | join("/") }}{% endif %}\`\` — {{ d.message }}
+{% endfor %}
+
 {% endif %}
 `,
     "export_tree.md.j2": `{#-

package/dist/workflow/_templates-bundled.js.map

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+{"version":3,"file":"_templates-bundled.js","sourceRoot":"","sources":["../../src/workflow/_templates-bundled.ts"],"names":[],"mappings":"AAAA,gEAAgE;AAChE,MAAM,CAAC,MAAM,iBAAiB,GAA2B;IACvD,eAAe,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA4DlB;IACC,kBAAkB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAiDrB;IACC,0BAA0B,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgC7B;IACC,sBAAsB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmDzB;IACC,mBAAmB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2BtB;IACC,iBAAiB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA+BpB;IACC,sBAAsB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA6BzB;IACC,sBAAsB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2BzB;IACC,qBAAqB,EAAE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAyDxB;CACA,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.3.0",
+  "version": "1.5.0",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -39,10 +39,10 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/connection-validation": "1.2.0",
-    "@galaxy-tool-util/core": "1.2.0",
-    "@galaxy-tool-util/schema": "1.2.0",
-    "@galaxy-tool-util/search": "1.2.0"
+    "@galaxy-tool-util/connection-validation": "1.5.0",
+    "@galaxy-tool-util/core": "1.5.0",
+    "@galaxy-tool-util/schema": "1.5.0",
+    "@galaxy-tool-util/search": "1.5.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",

package/spec/galaxy-tool-cache.json

@@ -156,22 +156,6 @@
           "description": "Galaxy instance URL for fallback"
         }
       ]
-    },
-    {
-      "name": "structural-schema",
-      "description": "Export the structural JSON Schema for Galaxy workflows",
-      "handler": "structuralSchema",
-      "options": [
-        {
-          "flags": "--format <fmt>",
-          "description": "Workflow format: format2 (default) or native",
-          "default": "format2"
-        },
-        {
-          "flags": "--output <file>",
-          "description": "Output file (default: stdout)"
-        }
-      ]
     }
   ]
 }

package/spec/gxwf.json

@@ -91,6 +91,83 @@
         }
       ]
     },
+    {
+      "name": "draft-validate",
+      "description": "Validate a draft Galaxy workflow (class: GalaxyWorkflowDraft)",
+      "handler": "draftValidate",
+      "args": [
+        {
+          "raw": "<file>",
+          "description": "Draft workflow file (.gxwf.yml)"
+        }
+      ],
+      "options": [
+        {
+          "flags": "--format <fmt>",
+          "description": "Force format: format2 (native is rejected for drafts)"
+        },
+        {
+          "flags": "--json",
+          "description": "Output structured JSON report"
+        },
+        {
+          "flags": "--report-html [file]",
+          "description": "Write HTML report to file (or stdout if omitted)"
+        },
+        {
+          "flags": "--report-markdown [file]",
+          "description": "Write Markdown report to file (or stdout if omitted)"
+        }
+      ]
+    },
+    {
+      "name": "_draft-extract",
+      "description": "Extract the concrete subset of a draft workflow (agent-loop internal; hidden)",
+      "handler": "draftExtract",
+      "hidden": true,
+      "args": [
+        {
+          "raw": "<file>",
+          "description": "Draft workflow file (.gxwf.yml)"
+        }
+      ],
+      "options": [
+        {
+          "flags": "-o, --output <file>",
+          "description": "Write extracted workflow to file (default: stdout)"
+        },
+        {
+          "flags": "--report-json [file]",
+          "description": "Write extraction report JSON (drops, rewrites, class flip) — to file or stdout if omitted"
+        },
+        {
+          "flags": "--format <fmt>",
+          "description": "Force input format: format2 (default; native is rejected)"
+        }
+      ]
+    },
+    {
+      "name": "draft-next-step",
+      "description": "Pick the next step a downstream agent should work on (or report no remaining work)",
+      "handler": "draftNextStep",
+      "args": [
+        {
+          "raw": "<file>",
+          "description": "Draft workflow file (.gxwf.yml)"
+        }
+      ],
+      "options": [
+        {
+          "flags": "--format <fmt>",
+          "description": "Force input format: format2 (default; native is rejected)"
+        },
+        {
+          "flags": "--output-format <fmt>",
+          "description": "Output format: json (default) or markdown",
+          "default": "json"
+        }
+      ]
+    },
     {
       "name": "clean",
       "description": "Strip stale keys and decode legacy tool_state encoding",
@@ -555,6 +632,48 @@
         }
       ]
     },
+    {
+      "name": "validate-tool-source",
+      "description": "Validate a user-defined Galaxy tool source YAML (class: GalaxyUserTool / GalaxyTool) against the Galaxy DynamicToolSources schema + #22615 semantic checks",
+      "handler": "validateToolSource",
+      "args": [
+        {
+          "raw": "<file>",
+          "description": "Tool source YAML file"
+        }
+      ],
+      "options": [
+        {
+          "flags": "--json",
+          "description": "Output structured JSON report"
+        },
+        {
+          "flags": "--schema-only",
+          "description": "Skip semantic (model_validator) checks; structural JSON-Schema validation only"
+        }
+      ]
+    },
+    {
+      "name": "validate-tool-source-tree",
+      "description": "Batch validate user-defined Galaxy tool source YAMLs (auto-discovered by class:) under a directory",
+      "handler": "validateToolSourceTree",
+      "args": [
+        {
+          "raw": "<dir>",
+          "description": "Directory to scan for tool source files"
+        }
+      ],
+      "options": [
+        {
+          "flags": "--json",
+          "description": "Output structured JSON report"
+        },
+        {
+          "flags": "--schema-only",
+          "description": "Skip semantic (model_validator) checks; structural JSON-Schema validation only"
+        }
+      ]
+    },
     {
       "name": "tool-search",
       "description": "Search the Galaxy Tool Shed for tools matching a query",
@@ -688,6 +807,22 @@
           "description": "Emit machine-readable JSON envelope"
         }
       ]
+    },
+    {
+      "name": "structural-schema",
+      "description": "Export the structural JSON Schema for Galaxy workflows",
+      "handler": "structuralSchema",
+      "options": [
+        {
+          "flags": "--format <fmt>",
+          "description": "Workflow format: format2 (default) or native",
+          "default": "format2"
+        },
+        {
+          "flags": "--output <file>",
+          "description": "Output file (default: stdout)"
+        }
+      ]
     }
   ]
 }