@galaxy-tool-util/cli 1.0.0 → 1.2.0

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

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

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

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

package/dist/bin/gxwf.js

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

package/dist/bin/gxwf.js.map

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

package/dist/commands/annotate-connections.d.ts

@@ -0,0 +1,30 @@
+/**
+ * Helper for `gxwf mermaid` / `gxwf cytoscapejs` `--annotate-connections`:
+ * runs the connection validator against a workflow and returns the
+ * `EdgeAnnotation` lookup the emitters consume.
+ */
+import { type EdgeAnnotation } from "@galaxy-tool-util/connection-validation";
+import type { ToolCache } from "@galaxy-tool-util/core";
+import type { ParsedTool } from "@galaxy-tool-util/schema";
+export interface ResolveEdgeAnnotationsOptions {
+    cacheDir?: string;
+}
+export declare function resolveEdgeAnnotations(data: Record<string, unknown>, opts?: ResolveEdgeAnnotationsOptions): Promise<Map<string, EdgeAnnotation>>;
+export declare function resolveEdgeAnnotationsWithCache(data: Record<string, unknown>, cache: ToolCache): Promise<Map<string, EdgeAnnotation>>;
+export interface ResolvedToolSpec {
+    tool_id: string;
+    tool_version: string;
+    parsed: ParsedTool;
+}
+/**
+ * Variant of `resolveEdgeAnnotationsWithCache` that also returns the
+ * `ParsedTool` specs the validator consumed, keyed by `toolId@toolVersion`.
+ * The hybrid `gxwf-web` edge-annotations response uses this so co-resident
+ * browsers can write the specs into IndexedDB and warm the client-side
+ * `useToolInfoService` for free.
+ */
+export declare function resolveEdgeAnnotationsAndSpecsWithCache(data: Record<string, unknown>, cache: ToolCache): Promise<{
+    annotations: Map<string, EdgeAnnotation>;
+    specs: Map<string, ResolvedToolSpec>;
+}>;
+//# sourceMappingURL=annotate-connections.d.ts.map

package/dist/commands/annotate-connections.d.ts.map

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

@@ -0,0 +1,42 @@
+/**
+ * Helper for `gxwf mermaid` / `gxwf cytoscapejs` `--annotate-connections`:
+ * runs the connection validator against a workflow and returns the
+ * `EdgeAnnotation` lookup the emitters consume.
+ */
+import { buildEdgeAnnotations, buildGetToolInfo as _buildGetToolInfo, buildWorkflowGraph, validateConnectionGraph, } from "@galaxy-tool-util/connection-validation";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { buildGetToolInfo } from "./connection-validation.js";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+export async function resolveEdgeAnnotations(data, opts = {}) {
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    return resolveEdgeAnnotationsWithCache(data, cache);
+}
+export async function resolveEdgeAnnotationsWithCache(data, cache) {
+    const getToolInfo = await buildGetToolInfo(data, cache);
+    const graph = buildWorkflowGraph(data, getToolInfo);
+    const [report] = validateConnectionGraph(graph);
+    return buildEdgeAnnotations(report);
+}
+/**
+ * Variant of `resolveEdgeAnnotationsWithCache` that also returns the
+ * `ParsedTool` specs the validator consumed, keyed by `toolId@toolVersion`.
+ * The hybrid `gxwf-web` edge-annotations response uses this so co-resident
+ * browsers can write the specs into IndexedDB and warm the client-side
+ * `useToolInfoService` for free.
+ */
+export async function resolveEdgeAnnotationsAndSpecsWithCache(data, cache) {
+    const specs = new Map();
+    const getToolInfo = await _buildGetToolInfo(data, async (id, version) => {
+        const r = await loadCachedTool(cache, id, version);
+        if (isResolveError(r))
+            return null;
+        const ver = r.tool.version ?? version ?? "";
+        specs.set(`${id}@${ver}`, { tool_id: id, tool_version: ver, parsed: r.tool });
+        return r.tool;
+    });
+    const graph = buildWorkflowGraph(data, getToolInfo);
+    const [report] = validateConnectionGraph(graph);
+    return { annotations: buildEdgeAnnotations(report), specs };
+}
+//# sourceMappingURL=annotate-connections.js.map

package/dist/commands/annotate-connections.js.map

@@ -0,0 +1 @@
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package/dist/commands/connection-validation.d.ts

@@ -0,0 +1,20 @@
+/**
+ * CLI integration for connection validation.
+ *
+ * Walks a workflow dict to collect every tool reference (recursing into
+ * subworkflows), preloads each tool from the cache, and runs
+ * `validateConnectionsReport`. The connection validator wants a sync
+ * `GetToolInfo` lookup, so async cache fetches happen up front.
+ *
+ * The walker + preloader live in `@galaxy-tool-util/connection-validation`
+ * (`collectToolRefs`, `buildGetToolInfo`); this module is a thin wrapper that
+ * adapts the CLI's on-disk `ToolCache` to the lifted helper's `AsyncToolFetcher`.
+ */
+import { collectToolRefs, type GetToolInfo } from "@galaxy-tool-util/connection-validation";
+import type { ToolCache } from "@galaxy-tool-util/core";
+import type { ConnectionValidationReport } from "@galaxy-tool-util/schema";
+export { collectToolRefs };
+export type { ToolRef } from "@galaxy-tool-util/connection-validation";
+export declare function buildConnectionReport(data: Record<string, unknown>, cache: ToolCache): Promise<ConnectionValidationReport>;
+export declare function buildGetToolInfo(data: Record<string, unknown>, cache: ToolCache): Promise<GetToolInfo>;
+//# sourceMappingURL=connection-validation.d.ts.map

package/dist/commands/connection-validation.d.ts.map

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

@@ -0,0 +1,26 @@
+/**
+ * CLI integration for connection validation.
+ *
+ * Walks a workflow dict to collect every tool reference (recursing into
+ * subworkflows), preloads each tool from the cache, and runs
+ * `validateConnectionsReport`. The connection validator wants a sync
+ * `GetToolInfo` lookup, so async cache fetches happen up front.
+ *
+ * The walker + preloader live in `@galaxy-tool-util/connection-validation`
+ * (`collectToolRefs`, `buildGetToolInfo`); this module is a thin wrapper that
+ * adapts the CLI's on-disk `ToolCache` to the lifted helper's `AsyncToolFetcher`.
+ */
+import { buildGetToolInfo as _buildGetToolInfo, collectToolRefs, validateConnectionsReport, } from "@galaxy-tool-util/connection-validation";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+export { collectToolRefs };
+export async function buildConnectionReport(data, cache) {
+    const getToolInfo = await buildGetToolInfo(data, cache);
+    return validateConnectionsReport(data, getToolInfo);
+}
+export async function buildGetToolInfo(data, cache) {
+    return _buildGetToolInfo(data, async (id, version) => {
+        const r = await loadCachedTool(cache, id, version);
+        return isResolveError(r) ? null : r.tool;
+    });
+}
+//# sourceMappingURL=connection-validation.js.map

package/dist/commands/connection-validation.js.map

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+{"version":3,"file":"connection-validation.js","sourceRoot":"","sources":["../../src/commands/connection-validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EACL,gBAAgB,IAAI,iBAAiB,EACrC,eAAe,EACf,yBAAyB,GAE1B,MAAM,yCAAyC,CAAC;AAIjD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AAEnE,OAAO,EAAE,eAAe,EAAE,CAAC;AAG3B,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,IAA6B,EAC7B,KAAgB;IAEhB,MAAM,WAAW,GAAG,MAAM,gBAAgB,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACxD,OAAO,yBAAyB,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC;AACtD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,IAA6B,EAC7B,KAAgB;IAEhB,OAAO,iBAAiB,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE;QACnD,MAAM,CAAC,GAAG,MAAM,cAAc,CAAC,KAAK,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC;QACnD,OAAO,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3C,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/commands/cytoscapejs/_template-bundled.d.ts

@@ -0,0 +1,2 @@
+export declare const CYTOSCAPE_HTML_TEMPLATE = "<!doctype html>\n\n<html>\n\n<head>\n    <title>Galaxy Workflow</title>\n    <script src=\"https://unpkg.com/cytoscape@3.33.2/dist/cytoscape.min.js\"></script>\n    <script src=\"https://unpkg.com/dagre@0.8.5/dist/dagre.min.js\"></script>\n    <script src=\"https://unpkg.com/cytoscape-dagre@2.5.0/cytoscape-dagre.js\"></script>\n    <script src=\"https://unpkg.com/@popperjs/core@2.11.8/dist/umd/popper.min.js\"></script>\n    <script src=\"https://unpkg.com/cytoscape-popper@2.0.0/cytoscape-popper.js\"></script>\n    <script src=\"https://unpkg.com/tippy.js@6.3.7/dist/tippy.umd.min.js\"></script>\n    <link rel=\"stylesheet\" href=\"https://unpkg.com/tippy.js@6.3.7/dist/tippy.css\" />\n    <script>\ndocument.addEventListener(\"DOMContentLoaded\", function() {\n    var requestedLayout = $layout;\n    var dagreReady = (typeof cytoscapeDagre !== 'undefined');\n    if (dagreReady && cytoscape.use) {\n        try { cytoscape.use(cytoscapeDagre); } catch (e) { /* already registered */ }\n    }\n    var layoutConfig = (function(name) {\n        if (name === 'dagre') {\n            return dagreReady\n                ? { name: 'dagre', rankDir: 'LR', nodeSep: 40, rankSep: 80 }\n                : { name: 'preset' };\n        }\n        if (name === 'breadthfirst') return { name: 'breadthfirst', directed: true, spacingFactor: 1.2 };\n        if (name === 'grid') return { name: 'grid' };\n        if (name === 'cose') return { name: 'cose' };\n        if (name === 'random') return { name: 'random' };\n        if (name === 'topological') return { name: 'preset' };\n        return { name: 'preset' };\n    })(requestedLayout);\n    var cy = cytoscape({\n        container: document.getElementById('cy'),\n        elements: $elements,\n        layout: layoutConfig,\n        // so we can see the ids\n        style: [\n            {\n                selector: 'node',\n                style: {\n                    'label': 'data(label)'\n                }\n            },\n            {\n                selector: 'edge',\n                style: {\n                    'curve-style': 'bezier',\n                    'target-arrow-shape': 'vee',\n                    'arrow-scale': 2\n                }\n            },\n            {\n                selector: \".input\",\n                style: {\n                    shape: 'diamond',\n                    'background-color': '#d0bb46'\n                }\n            },\n            {\n                selector: \".runnable\",\n                style: {\n                    shape: 'round-rectangle',\n                    'background-color': '#2c3143'\n                }\n            },\n            {\n                selector: 'edge.mapover_1',\n                style: { width: 4, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.mapover_2',\n                style: { width: 6, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.mapover_3',\n                style: { width: 8, 'line-color': '#5a8' }\n            },\n            {\n                selector: 'edge.reduction',\n                style: {\n                    'line-style': 'dashed',\n                    'line-color': '#a55',\n                    'target-arrow-shape': 'tee',\n                    'target-arrow-color': '#a55'\n                }\n            }\n        ]\n      });\n\n  function makePopper(ele) {\n    let ref = ele.popperRef(); // used only for positioning\n    let dummyDomEle = document.createElement('div');\n\n    ele.tippy = tippy(dummyDomEle, { // tippy options:\n      getReferenceClientRect: ref.getBoundingClientRect.bind(ref),\n      content: function() {\n        let content = document.createElement('div');\n\n        let innerHTML = '';\n        if(ele.isNode()) {\n            let stepType = ele.data(\"step_type\");\n            innerHTML +=  \"<p><i>Step Type:</i> \" + stepType + \"</p>\";\n            let toolId = ele.data(\"tool_id\");\n            if (toolId) {\n                innerHTML +=  \"<p><i>ToolID:</i> \" + toolId + \"</p>\";\n            }\n            let repoLink = ele.data(\"repo_link\");\n            if (repoLink) {\n                innerHTML += \"<a href=\" + repoLink + '\">Visit Tool Shed Repository</a>';\n            }\n            let doc = ele.data('doc');\n            if (doc) {\n                innerHTML += \"<p>\" + doc + \"</p>\";\n            }\n        } else {\n            let output = ele.data(\"output\");\n            let input = ele.data(\"input\");\n            if(output) {\n                innerHTML += \"Output named \" + output + \" connects to \" + input;\n            } else {\n                innerHTML += \"Connected to input \" + input;\n            }\n            let mapDepth = ele.data(\"map_depth\");\n            if (mapDepth) {\n                let mapping = ele.data(\"mapping\");\n                innerHTML += \"<p><i>Map depth:</i> \" + mapDepth + (mapping ? \" (\" + mapping + \")\" : \"\") + \"</p>\";\n            }\n            if (ele.data(\"reduction\")) {\n                innerHTML += \"<p><i>Reduction:</i> list \u2192 multi-data</p>\";\n            }\n        }\n        content.innerHTML = innerHTML;\n\n        return content;\n      },\n      delay: [0,1000],\n      interactive: true,\n      placement: 'bottom',\n      trigger: 'manual', // probably want manual mode\n      appendTo: document.body\n    });\n  }\n\n cy.ready(function() {\n    cy.elements().forEach(function(ele) {\n      makePopper(ele);\n    });\n  });\n\n  cy.elements().unbind('mouseover');\n  cy.elements().bind('mouseover', function(event) { event.target.tippy.show(); });\n\n  cy.elements().unbind('mouseout');\n  cy.elements().bind('mouseout', function(event) { event.target.tippy.hide(); });\n  // document.querySelector('#cypng').setAttribute('src', cy.png());\n});\n\n    </script>\n</head>\n\n<style>\n    #cy {\n        width: 100%;\n        height: 100%;\n        position: absolute;\n        top: 0px;\n        left: 0px;\n    }\n    a {\n        color: #d0bb46\n    }\n</style>\n\n<body>\n    <div id=\"cy\"></div>\n</body>\n</html>\n";
+//# sourceMappingURL=_template-bundled.d.ts.map

package/dist/commands/cytoscapejs/_template-bundled.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"_template-bundled.d.ts","sourceRoot":"","sources":["../../../src/commands/cytoscapejs/_template-bundled.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,uBAAuB,s/LAmLnC,CAAC"}

package/dist/commands/cytoscapejs/_template-bundled.js

@@ -0,0 +1,182 @@
+// AUTO-GENERATED by scripts/bundle-templates.mjs — do not edit.
+export const CYTOSCAPE_HTML_TEMPLATE = `<!doctype html>
+
+<html>
+
+<head>
+    <title>Galaxy Workflow</title>
+    <script src="https://unpkg.com/cytoscape@3.33.2/dist/cytoscape.min.js"></script>
+    <script src="https://unpkg.com/dagre@0.8.5/dist/dagre.min.js"></script>
+    <script src="https://unpkg.com/cytoscape-dagre@2.5.0/cytoscape-dagre.js"></script>
+    <script src="https://unpkg.com/@popperjs/core@2.11.8/dist/umd/popper.min.js"></script>
+    <script src="https://unpkg.com/cytoscape-popper@2.0.0/cytoscape-popper.js"></script>
+    <script src="https://unpkg.com/tippy.js@6.3.7/dist/tippy.umd.min.js"></script>
+    <link rel="stylesheet" href="https://unpkg.com/tippy.js@6.3.7/dist/tippy.css" />
+    <script>
+document.addEventListener("DOMContentLoaded", function() {
+    var requestedLayout = $layout;
+    var dagreReady = (typeof cytoscapeDagre !== 'undefined');
+    if (dagreReady && cytoscape.use) {
+        try { cytoscape.use(cytoscapeDagre); } catch (e) { /* already registered */ }
+    }
+    var layoutConfig = (function(name) {
+        if (name === 'dagre') {
+            return dagreReady
+                ? { name: 'dagre', rankDir: 'LR', nodeSep: 40, rankSep: 80 }
+                : { name: 'preset' };
+        }
+        if (name === 'breadthfirst') return { name: 'breadthfirst', directed: true, spacingFactor: 1.2 };
+        if (name === 'grid') return { name: 'grid' };
+        if (name === 'cose') return { name: 'cose' };
+        if (name === 'random') return { name: 'random' };
+        if (name === 'topological') return { name: 'preset' };
+        return { name: 'preset' };
+    })(requestedLayout);
+    var cy = cytoscape({
+        container: document.getElementById('cy'),
+        elements: $elements,
+        layout: layoutConfig,
+        // so we can see the ids
+        style: [
+            {
+                selector: 'node',
+                style: {
+                    'label': 'data(label)'
+                }
+            },
+            {
+                selector: 'edge',
+                style: {
+                    'curve-style': 'bezier',
+                    'target-arrow-shape': 'vee',
+                    'arrow-scale': 2
+                }
+            },
+            {
+                selector: ".input",
+                style: {
+                    shape: 'diamond',
+                    'background-color': '#d0bb46'
+                }
+            },
+            {
+                selector: ".runnable",
+                style: {
+                    shape: 'round-rectangle',
+                    'background-color': '#2c3143'
+                }
+            },
+            {
+                selector: 'edge.mapover_1',
+                style: { width: 4, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.mapover_2',
+                style: { width: 6, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.mapover_3',
+                style: { width: 8, 'line-color': '#5a8' }
+            },
+            {
+                selector: 'edge.reduction',
+                style: {
+                    'line-style': 'dashed',
+                    'line-color': '#a55',
+                    'target-arrow-shape': 'tee',
+                    'target-arrow-color': '#a55'
+                }
+            }
+        ]
+      });
+
+  function makePopper(ele) {
+    let ref = ele.popperRef(); // used only for positioning
+    let dummyDomEle = document.createElement('div');
+
+    ele.tippy = tippy(dummyDomEle, { // tippy options:
+      getReferenceClientRect: ref.getBoundingClientRect.bind(ref),
+      content: function() {
+        let content = document.createElement('div');
+
+        let innerHTML = '';
+        if(ele.isNode()) {
+            let stepType = ele.data("step_type");
+            innerHTML +=  "<p><i>Step Type:</i> " + stepType + "</p>";
+            let toolId = ele.data("tool_id");
+            if (toolId) {
+                innerHTML +=  "<p><i>ToolID:</i> " + toolId + "</p>";
+            }
+            let repoLink = ele.data("repo_link");
+            if (repoLink) {
+                innerHTML += "<a href=" + repoLink + '">Visit Tool Shed Repository</a>';
+            }
+            let doc = ele.data('doc');
+            if (doc) {
+                innerHTML += "<p>" + doc + "</p>";
+            }
+        } else {
+            let output = ele.data("output");
+            let input = ele.data("input");
+            if(output) {
+                innerHTML += "Output named " + output + " connects to " + input;
+            } else {
+                innerHTML += "Connected to input " + input;
+            }
+            let mapDepth = ele.data("map_depth");
+            if (mapDepth) {
+                let mapping = ele.data("mapping");
+                innerHTML += "<p><i>Map depth:</i> " + mapDepth + (mapping ? " (" + mapping + ")" : "") + "</p>";
+            }
+            if (ele.data("reduction")) {
+                innerHTML += "<p><i>Reduction:</i> list → multi-data</p>";
+            }
+        }
+        content.innerHTML = innerHTML;
+
+        return content;
+      },
+      delay: [0,1000],
+      interactive: true,
+      placement: 'bottom',
+      trigger: 'manual', // probably want manual mode
+      appendTo: document.body
+    });
+  }
+
+ cy.ready(function() {
+    cy.elements().forEach(function(ele) {
+      makePopper(ele);
+    });
+  });
+
+  cy.elements().unbind('mouseover');
+  cy.elements().bind('mouseover', function(event) { event.target.tippy.show(); });
+
+  cy.elements().unbind('mouseout');
+  cy.elements().bind('mouseout', function(event) { event.target.tippy.hide(); });
+  // document.querySelector('#cypng').setAttribute('src', cy.png());
+});
+
+    </script>
+</head>
+
+<style>
+    #cy {
+        width: 100%;
+        height: 100%;
+        position: absolute;
+        top: 0px;
+        left: 0px;
+    }
+    a {
+        color: #d0bb46
+    }
+</style>
+
+<body>
+    <div id="cy"></div>
+</body>
+</html>
+`;
+//# sourceMappingURL=_template-bundled.js.map

package/dist/commands/cytoscapejs/_template-bundled.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"_template-bundled.js","sourceRoot":"","sources":["../../../src/commands/cytoscapejs/_template-bundled.ts"],"names":[],"mappings":"AAAA,gEAAgE;AAChE,MAAM,CAAC,MAAM,uBAAuB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmLtC,CAAC"}

package/dist/commands/cytoscapejs.d.ts

@@ -0,0 +1,12 @@
+import type { CytoscapeElements, LayoutName } from "@galaxy-tool-util/schema";
+export interface CytoscapeJsCommandOptions {
+    output?: string;
+    html?: boolean;
+    json?: boolean;
+    annotateConnections?: boolean;
+    cacheDir?: string;
+    layout?: string;
+}
+export declare function renderHtml(elements: CytoscapeElements, layout?: LayoutName): string;
+export declare function runCytoscapeJs(filePath: string, opts: CytoscapeJsCommandOptions): Promise<void>;
+//# sourceMappingURL=cytoscapejs.d.ts.map

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

@@ -0,0 +1 @@
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