@galaxyproject/orbit 0.0.0 → 0.9.0

package/extensions/orbit/vendor/skills/summarize-galaxy-workflow/_verify.json

@@ -0,0 +1,17 @@
+{
+  "verify_schema_version": 1,
+  "entries": [
+    {
+      "artifact_id": "summary-galaxy-workflow",
+      "direction": "output",
+      "kind": "json",
+      "default_filename": "summary-galaxy-workflow.json",
+      "schema": "[[summary-galaxy-workflow]]",
+      "validator_bin": "foundry",
+      "args": [
+        "validate-summary-galaxy-workflow",
+        "{artifact_path}"
+      ]
+    }
+  ]
+}

package/extensions/orbit/vendor/skills/summarize-galaxy-workflow/references/cli/convert.json

@@ -0,0 +1,123 @@
+{
+  "type": "cli-command",
+  "tool": "gxwf",
+  "command": "convert",
+  "summary": "Convert a Galaxy workflow between native (.ga) and format2 (.gxwf.yml) representations.",
+  "source_path": "content/cli/gxwf/convert.md",
+  "source_revision": 2,
+  "package": "@galaxy-tool-util/cli",
+  "description": "Convert between native (.ga) and format2 (.gxwf.yml) formats",
+  "synopsis": "gxwf convert [options] <file>",
+  "args": [
+    {
+      "raw": "file",
+      "name": "file",
+      "required": true,
+      "variadic": false,
+      "description": "Workflow file (.ga, .gxwf.yml)"
+    }
+  ],
+  "options": [
+    {
+      "flags": "--to <format>",
+      "name": "to",
+      "description": "Target format: native or format2 (infers opposite by default)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<format>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--output <file>",
+      "name": "output",
+      "description": "Write result to file (default: stdout)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<file>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--compact",
+      "name": "compact",
+      "description": "Omit position info in format2 output",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--json",
+      "name": "json",
+      "description": "Force JSON output",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--yaml",
+      "name": "yaml",
+      "description": "Force YAML output",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--format <fmt>",
+      "name": "format",
+      "description": "Force source format (auto-detected by default)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<fmt>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--stateful",
+      "name": "stateful",
+      "description": "Use cached tool definitions for schema-aware state re-encoding",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--cache-dir <dir>",
+      "name": "cacheDir",
+      "description": "Tool cache directory (for --stateful)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<dir>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict",
+      "name": "strict",
+      "description": "Shorthand for --strict-structure --strict-encoding --strict-state",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-structure",
+      "name": "strictStructure",
+      "description": "Reject unknown keys at envelope/step level",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-encoding",
+      "name": "strictEncoding",
+      "description": "Reject JSON-string tool_state and format2 field misuse",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-state",
+      "name": "strictState",
+      "description": "Require every tool step to validate; no skips allowed",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    }
+  ],
+  "body": "# `gxwf convert`\n\nConvert a Galaxy workflow between the native `.ga` JSON and the `.gxwf.yml` format2 representation. Use this to normalize fetched IWC workflows into a consistent comparison representation.\n\n## Output\n\nDefault output is the converted workflow on stdout. With `--output`, the result is written to a file. JSON output is selected with `--json` (or `--to native`); YAML output is selected with `--yaml` (or `--to format2`).\n\n## Examples\n\n```bash\ngxwf convert workflow.ga --to format2 --output workflow.gxwf.yml\ngxwf convert workflow.ga --to format2 --compact\ngxwf convert workflow.gxwf.yml --to native --output workflow.ga\n```\n\n## Gotchas\n\n- Default output is stdout; pipe or pass `--output` when persisting.\n- `--compact` drops node position metadata; useful for structural diffs and skeleton generation.\n- `--stateful` requires a populated tool cache (see `galaxy-tool-cache`); without it, tool-state stays as fetched."
+}

package/extensions/orbit/vendor/skills/summarize-galaxy-workflow/references/cli/foundry.md

@@ -0,0 +1,25 @@
+---
+type: cli-tool
+tool: foundry
+origin: npm
+package: "@galaxy-foundry/gxwf-foundry"
+invoke: foundry
+invoke_fallback: "npx --package @galaxy-foundry/gxwf-foundry foundry"
+availability_check: "foundry --help"
+docs_url: "https://github.com/galaxyproject/foundry/blob/main/packages/gxwf-foundry/README.md"
+tags:
+  - cli/foundry
+status: draft
+created: 2026-05-11
+revised: 2026-05-11
+revision: 1
+summary: "Foundry CLI: bundles all Mold IO validators and a summarize-nextflow subcommand."
+---
+
+# foundry
+
+Unified Foundry CLI. Subcommands cover every Mold IO validator plus a `summarize-nextflow` wrapper around the standalone `@galaxy-foundry/summarize-nextflow` package. Per-subcommand synopsis, args, and options are rendered from `@galaxy-foundry/gxwf-foundry/meta`.
+
+## Install
+
+`npx --package @galaxy-foundry/gxwf-foundry foundry <subcommand>` runs without a global install. For repeat use, `npm install -g @galaxy-foundry/gxwf-foundry`.

package/extensions/orbit/vendor/skills/summarize-galaxy-workflow/references/cli/validate.json

@@ -0,0 +1,142 @@
+{
+  "type": "cli-command",
+  "tool": "gxwf",
+  "command": "validate",
+  "summary": "Validate Galaxy workflow structure, tool state, and optional connection compatibility before runtime execution.",
+  "source_path": "content/cli/gxwf/validate.md",
+  "source_revision": 3,
+  "package": "@galaxy-tool-util/cli",
+  "description": "Validate Galaxy workflow files (structure + optional tool state)",
+  "synopsis": "gxwf validate [options] <file>",
+  "args": [
+    {
+      "raw": "file",
+      "name": "file",
+      "required": true,
+      "variadic": false,
+      "description": "Workflow file (.ga, .gxwf.yml)"
+    }
+  ],
+  "options": [
+    {
+      "flags": "--format <fmt>",
+      "name": "format",
+      "description": "Force format: native or format2 (auto-detected by default)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<fmt>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--no-tool-state",
+      "name": "toolState",
+      "description": "Skip tool state validation",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": true
+    },
+    {
+      "flags": "--cache-dir <dir>",
+      "name": "cacheDir",
+      "description": "Tool cache directory",
+      "takesArgument": true,
+      "argumentPlaceholder": "<dir>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--offline",
+      "name": "offline",
+      "description": "Do not fetch uncached tools; read only the local cache (uncached tools are skipped)",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--galaxy-url <url>",
+      "name": "galaxyUrl",
+      "description": "Galaxy instance to try as a tool source after the ToolShed when fetching uncached tools",
+      "takesArgument": true,
+      "argumentPlaceholder": "<url>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--mode <mode>",
+      "name": "mode",
+      "description": "Validation backend: effect (default) or json-schema",
+      "takesArgument": true,
+      "argumentPlaceholder": "<mode>",
+      "optionalArgument": false,
+      "negatable": false,
+      "defaultValue": "effect"
+    },
+    {
+      "flags": "--tool-schema-dir <dir>",
+      "name": "toolSchemaDir",
+      "description": "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)",
+      "takesArgument": true,
+      "argumentPlaceholder": "<dir>",
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--json",
+      "name": "json",
+      "description": "Output structured JSON report",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--report-html [file]",
+      "name": "reportHtml",
+      "description": "Write HTML report to file (or stdout if omitted)",
+      "takesArgument": true,
+      "argumentPlaceholder": "[file]",
+      "optionalArgument": true,
+      "negatable": false
+    },
+    {
+      "flags": "--connections",
+      "name": "connections",
+      "description": "Validate connection-type compatibility (collection algebra, map-over)",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict",
+      "name": "strict",
+      "description": "Shorthand for --strict-structure --strict-encoding --strict-state",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-structure",
+      "name": "strictStructure",
+      "description": "Reject unknown keys at envelope/step level",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-encoding",
+      "name": "strictEncoding",
+      "description": "Reject JSON-string tool_state and format2 field misuse",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    },
+    {
+      "flags": "--strict-state",
+      "name": "strictState",
+      "description": "Require every tool step to validate; no skips allowed",
+      "takesArgument": false,
+      "optionalArgument": false,
+      "negatable": false
+    }
+  ],
+  "body": "# `gxwf validate`\n\nValidate a Galaxy workflow source file before attempting runtime execution. Use this as the design-time guardrail after step implementation and again after final workflow assembly.\n\n## Output\n\nDefault output is human-readable diagnostics. JSON output should be treated as the preferred cast-skill interface; free-text diagnostics are a fallback for humans.\n\n## Examples\n\n```bash\ngxwf validate workflow.ga\ngxwf validate workflow.gxwf.yml --json\ngxwf validate workflow.gxwf.yml --json --connections --strict\ngxwf validate workflow.ga --mode json-schema --tool-schema-dir ./tool-schemas --json\n```\n\n## Gotchas\n\n- Validation is design-time structure checking. It does not prove that a workflow test will pass under Planemo.\n- Run after each generated Galaxy step when the harness can still attribute failures to the fresh step.\n- Run again after assembly to catch cross-step or workflow-level issues before runtime testing.\n- Prefer `--json` whenever a cast skill or harness needs to classify diagnostics.\n- Use `--connections` when tool cache metadata is available and data-shape compatibility matters, especially around collections and map-over.\n- `--no-tool-state` weakens validation. If used, record why tool metadata was unavailable and rerun without it before final runtime testing."
+}