@galaxy-tool-util/cli 1.4.0 → 1.6.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.4.0",
+  "version": "1.6.0",
   "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": "1.6.0",
+    "@galaxy-tool-util/core": "1.6.0",
+    "@galaxy-tool-util/schema": "1.6.0",
+    "@galaxy-tool-util/search": "1.6.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",

package/spec/gxwf.json

@@ -91,6 +91,99 @@
         }
       ]
     },
+    {
+      "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)"
+        },
+        {
+          "flags": "--concrete",
+          "description": "Additionally extract the concrete subset and run the regular `gxwf validate` checks on it"
+        },
+        {
+          "flags": "--cache-dir <dir>",
+          "description": "Tool cache directory (for --concrete tool-state validation)"
+        },
+        {
+          "flags": "--no-tool-state",
+          "description": "Skip tool-state validation in the --concrete pass (default: enabled when --concrete is set)"
+        },
+        {
+          "flags": "--connections",
+          "description": "Validate connection-type compatibility on the --concrete subset (collection algebra, map-over)"
+        }
+      ],
+      "optionGroups": ["strict"]
+    },
+    {
+      "name": "draft-extract",
+      "description": "Extract the concrete subset of a draft workflow (drop drafty steps, strip _plan_* fields, promote class when fully concrete)",
+      "handler": "draftExtract",
+      "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 +648,48 @@
         }
       ]
     },
+    {
+      "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",