@galaxy-tool-util/schema 1.13.1 → 1.15.0

package/dist/user-tool-source/schema.generated.d.ts

@@ -1,6 +1,7 @@
 export declare const userToolSourceSchema: {
     readonly $defs: {
         readonly Citation: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly content: {
                     readonly title: "Content";
@@ -32,6 +33,7 @@ export declare const userToolSourceSchema: {
             readonly type: "object";
         };
         readonly Container: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly container_id: {
                     readonly title: "Container Id";
@@ -48,6 +50,7 @@ export declare const userToolSourceSchema: {
             readonly type: "object";
         };
         readonly ContainerRequirement: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly container: {
                     readonly $ref: "#/$defs/Container";
@@ -64,9 +67,14 @@ export declare const userToolSourceSchema: {
         };
         readonly EmptyFieldParameterValidatorModel: {
             readonly additionalProperties: false;
+            readonly description: "Require a value that is neither an empty string nor null.";
+            readonly examples: readonly [{
+                readonly type: "empty_field";
+            }];
             readonly properties: {
                 readonly implicit: {
                     readonly default: false;
+                    readonly description: "Set internally when Galaxy added the validator automatically; tool authors normally leave this false.";
                     readonly title: "Implicit";
                     readonly type: "boolean";
                 };
@@ -77,26 +85,40 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Error message shown when validation fails; `%s` is replaced with the rejected value.";
                     readonly title: "Message";
                 };
                 readonly negate: {
                     readonly default: false;
+                    readonly description: "Require the value to be empty or null instead.";
                     readonly title: "Negate";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "empty_field";
                     readonly default: "empty_field";
+                    readonly description: "Fails validation when the submitted value is an empty string or null.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
             };
             readonly title: "EmptyFieldParameterValidatorModel";
             readonly type: "object";
+            readonly "x-parameter-example": {
+                readonly label: "Sample name";
+                readonly name: "sample_name";
+                readonly type: "text";
+                readonly validators: readonly [{
+                    readonly type: "empty_field";
+                }];
+            };
         };
         readonly FilePatternDatasetCollectionDescription: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly assign_primary_output: {
+                    readonly default: false;
+                    readonly description: "Whether the first matching file replaces the primary dataset output.";
                     readonly title: "Assign Primary Output";
                     readonly type: "boolean";
                 };
@@ -106,10 +128,14 @@ export declare const userToolSourceSchema: {
                     }, {
                         readonly type: "null";
                     }];
+                    readonly default: null;
+                    readonly description: "Directory to search, relative to the job working directory.";
                     readonly title: "Directory";
                 };
                 readonly discover_via: {
                     readonly const: "pattern";
+                    readonly default: "pattern";
+                    readonly description: "Discover datasets by matching files produced by the command.";
                     readonly title: "Discover Via";
                     readonly type: "string";
                 };
@@ -119,45 +145,60 @@ export declare const userToolSourceSchema: {
                     }, {
                         readonly type: "null";
                     }];
+                    readonly default: null;
+                    readonly description: "Galaxy datatype extension assigned to each discovered dataset.";
                     readonly title: "Format";
                 };
                 readonly match_relative_path: {
+                    readonly default: false;
+                    readonly description: "Whether `pattern` matches each file's relative path instead of only its filename.";
                     readonly title: "Match Relative Path";
                     readonly type: "boolean";
                 };
                 readonly pattern: {
+                    readonly description: "Regular expression matched against produced filenames. Named groups such as `name`, `designation`, `ext`, and `dbkey` set discovered dataset metadata.";
                     readonly title: "Pattern";
                     readonly type: "string";
                 };
                 readonly recurse: {
+                    readonly default: false;
+                    readonly description: "Whether to search recursively below `directory`.";
                     readonly title: "Recurse";
                     readonly type: "boolean";
                 };
                 readonly sort_comp: {
+                    readonly default: "lexical";
+                    readonly description: "Whether the sort key is compared as text or as a number.";
                     readonly enum: readonly ["lexical", "numeric"];
                     readonly title: "Sort Comp";
                     readonly type: "string";
                 };
                 readonly sort_key: {
+                    readonly default: "filename";
+                    readonly description: "Discovered metadata used to order matching files.";
                     readonly enum: readonly ["filename", "name", "designation", "dbkey"];
                     readonly title: "Sort Key";
                     readonly type: "string";
                 };
                 readonly sort_reverse: {
                     readonly default: false;
+                    readonly description: "Whether to reverse the discovered dataset order.";
                     readonly title: "Sort Reverse";
                     readonly type: "boolean";
                 };
                 readonly visible: {
+                    readonly default: false;
+                    readonly description: "Whether discovered datasets are visible in the history.";
                     readonly title: "Visible";
                     readonly type: "boolean";
                 };
             };
-            readonly required: readonly ["discover_via", "format", "visible", "assign_primary_output", "directory", "recurse", "match_relative_path", "sort_key", "sort_comp", "pattern"];
+            readonly required: readonly ["pattern"];
             readonly title: "FilePatternDatasetCollectionDescription";
             readonly type: "object";
         };
         readonly HelpContent: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly content: {
                     readonly title: "Content";
@@ -175,19 +216,28 @@ export declare const userToolSourceSchema: {
         };
         readonly InRangeParameterValidatorModel: {
             readonly additionalProperties: false;
+            readonly description: "Require a numeric value to fall within optional lower and upper bounds.";
+            readonly examples: readonly [{
+                readonly max: 1;
+                readonly min: 0;
+                readonly type: "in_range";
+            }];
             readonly properties: {
                 readonly exclude_max: {
                     readonly default: false;
+                    readonly description: "Whether a value equal to `max` is rejected.";
                     readonly title: "Exclude Max";
                     readonly type: "boolean";
                 };
                 readonly exclude_min: {
                     readonly default: false;
+                    readonly description: "Whether a value equal to `min` is rejected.";
                     readonly title: "Exclude Min";
                     readonly type: "boolean";
                 };
                 readonly implicit: {
                     readonly default: false;
+                    readonly description: "Set internally when Galaxy added the validator automatically; tool authors normally leave this false.";
                     readonly title: "Implicit";
                     readonly type: "boolean";
                 };
@@ -200,6 +250,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects larger values; omit to leave the range without an upper bound.";
                     readonly title: "Max";
                 };
                 readonly message: {
@@ -209,6 +260,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Error message shown when validation fails; `%s` is replaced with the rejected value.";
                     readonly title: "Message";
                 };
                 readonly min: {
@@ -220,24 +272,43 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects smaller values; omit to leave the range without a lower bound.";
                     readonly title: "Min";
                 };
                 readonly negate: {
                     readonly default: false;
+                    readonly description: "Reject values inside the configured range instead of values outside it.";
                     readonly title: "Negate";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "in_range";
                     readonly default: "in_range";
+                    readonly description: "Enforces the numeric boundaries configured by `min` and `max`.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
             };
             readonly title: "InRangeParameterValidatorModel";
             readonly type: "object";
+            readonly "x-parameter-example": {
+                readonly label: "Score threshold";
+                readonly name: "threshold";
+                readonly type: "float";
+                readonly validators: readonly [{
+                    readonly max: 1;
+                    readonly min: 0;
+                    readonly type: "in_range";
+                }];
+                readonly value: 0.5;
+            };
         };
-        readonly IncomingToolOutputCollection: {
+        readonly IncomingToolOutputBoolean: {
+            readonly description: "A boolean value emitted as a workflow-visible scalar output.";
+            readonly examples: readonly [{
+                readonly name: "matched";
+                readonly type: "boolean";
+            }];
             readonly properties: {
                 readonly hidden: {
                     readonly anyOf: readonly [{
@@ -256,9 +327,125 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
+                    readonly title: "Label";
+                };
+                readonly name: {
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                    readonly type: "string";
+                };
+                readonly type: {
+                    readonly const: "boolean";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["name", "type"];
+            readonly title: "IncomingToolOutputBoolean";
+            readonly type: "object";
+        };
+        readonly IncomingToolOutputCollection: {
+            readonly additionalProperties: false;
+            readonly description: "A dataset collection populated by discovering files produced by the command.";
+            readonly examples: readonly [{
+                readonly collection_type: "list";
+                readonly discover_datasets: readonly [{
+                    readonly format: "txt";
+                    readonly pattern: "(?P<name>.+)\\.txt";
+                }];
+                readonly label: "Results";
+                readonly name: "results";
+                readonly type: "collection";
+            }];
+            readonly properties: {
+                readonly collection_type: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Fixed structure Galaxy creates for this output, such as `list`, `paired`, or a nested type such as `list:paired`.";
+                    readonly title: "Collection Type";
+                };
+                readonly collection_type_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Declared data-collection input whose runtime structure determines this output's collection type.";
+                    readonly title: "Collection Type Source";
+                };
+                readonly discover_datasets: {
+                    readonly anyOf: readonly [{
+                        readonly items: {
+                            readonly anyOf: readonly [{
+                                readonly $ref: "#/$defs/FilePatternDatasetCollectionDescription";
+                            }, {
+                                readonly $ref: "#/$defs/ToolProvidedMetadataDatasetCollection";
+                            }];
+                        };
+                        readonly type: "array";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Rules used to discover and populate collection elements from produced files.";
+                    readonly title: "Discover Datasets";
+                };
+                readonly format: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Default datatype extension assigned to collection elements.";
+                    readonly title: "Format";
+                };
+                readonly format_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Input whose datatype supplies the default format for collection elements.";
+                    readonly title: "Format Source";
+                };
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Hide the output in the history. The dataset is still created and usable by other tools and workflows.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
                     readonly title: "Label";
                 };
+                readonly metadata_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Dataset input whose metadata supplies defaults for collection elements.";
+                    readonly title: "Metadata Source";
+                };
                 readonly name: {
                     readonly anyOf: readonly [{
                         readonly type: "string";
@@ -266,23 +453,39 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
                     readonly title: "Name";
                 };
-                readonly structure: {
-                    readonly $ref: "#/$defs/ToolOutputCollectionStructure";
+                readonly structured_like: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Declared input whose element count, identifiers, and nesting this output mirrors. Use this when each produced element corresponds to an input element.";
+                    readonly title: "Structured Like";
                 };
                 readonly type: {
                     readonly const: "collection";
+                    readonly description: "Creates one history dataset collection populated from files produced by the command.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
             };
-            readonly required: readonly ["type", "structure"];
+            readonly required: readonly ["type"];
             readonly title: "IncomingToolOutputCollection";
             readonly type: "object";
         };
         readonly IncomingToolOutputDataset: {
+            readonly description: "A dataset collected from a file produced in the job working directory.";
+            readonly examples: readonly [{
+                readonly format: "txt";
+                readonly from_work_dir: "result.txt";
+                readonly label: "Result";
+                readonly name: "result";
+                readonly type: "data";
+            }];
             readonly properties: {
                 readonly discover_datasets: {
                     readonly anyOf: readonly [{
@@ -298,6 +501,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rules for discovering additional datasets produced by the command.";
                     readonly title: "Discover Datasets";
                 };
                 readonly format: {
@@ -307,7 +511,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "The short name for the output datatype.";
+                    readonly description: "Galaxy datatype extension assigned when the command always produces a fixed representation. Use `format_source` instead when the datatype depends on an input.";
                     readonly title: "Format";
                 };
                 readonly format_source: {
@@ -317,7 +521,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.";
+                    readonly description: "Data or collection input whose datatype extension this output inherits. Use this when the command preserves the input representation, such as filtering reads without changing their format.";
                     readonly title: "Format Source";
                 };
                 readonly from_work_dir: {
@@ -327,7 +531,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Relative path to a file produced by the tool in its working directory. Output’s contents are set to this file’s contents.";
+                    readonly description: "Relative path, inside the job working directory, that the command writes for this output. Galaxy claims that file after the command finishes.";
                     readonly title: "from_work_dir";
                 };
                 readonly hidden: {
@@ -337,7 +541,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "If true, the output will not be shown in the history.";
+                    readonly description: "Hide the output in the history. The dataset is still created and usable by other tools and workflows.";
                     readonly title: "Hidden";
                 };
                 readonly label: {
@@ -347,7 +551,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
                     readonly title: "Label";
                 };
                 readonly metadata_source: {
@@ -357,7 +561,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "This copies the metadata information from the tool’s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.";
+                    readonly description: "Data input whose datatype-specific metadata this output copies as defaults. Use this when the command preserves metadata Galaxy cannot infer from the output, such as interval column assignments.";
                     readonly title: "Metadata Source";
                 };
                 readonly name: {
@@ -367,7 +571,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
                     readonly title: "Name";
                 };
                 readonly precreate_directory: {
@@ -377,10 +581,12 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: false;
+                    readonly description: "Set true when `from_work_dir` names a produced directory for a composite datatype. Galaxy copies the directory contents into the output dataset's extra-files area.";
                     readonly title: "Precreate Directory";
                 };
                 readonly type: {
                     readonly const: "data";
+                    readonly description: "Creates one history dataset from a file produced by the command.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -389,12 +595,549 @@ export declare const userToolSourceSchema: {
             readonly title: "IncomingToolOutputDataset";
             readonly type: "object";
         };
+        readonly IncomingToolOutputFloat: {
+            readonly description: "A floating-point value emitted as a workflow-visible scalar output.";
+            readonly examples: readonly [{
+                readonly name: "score";
+                readonly type: "float";
+            }];
+            readonly properties: {
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "If true, the output will not be shown in the history.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
+                    readonly title: "Label";
+                };
+                readonly name: {
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                    readonly type: "string";
+                };
+                readonly type: {
+                    readonly const: "float";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["name", "type"];
+            readonly title: "IncomingToolOutputFloat";
+            readonly type: "object";
+        };
+        readonly IncomingToolOutputInteger: {
+            readonly description: "An integer value emitted as a workflow-visible scalar output.";
+            readonly examples: readonly [{
+                readonly name: "match_count";
+                readonly type: "integer";
+            }];
+            readonly properties: {
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "If true, the output will not be shown in the history.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
+                    readonly title: "Label";
+                };
+                readonly name: {
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                    readonly type: "string";
+                };
+                readonly type: {
+                    readonly const: "integer";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["name", "type"];
+            readonly title: "IncomingToolOutputInteger";
+            readonly type: "object";
+        };
+        readonly IncomingToolOutputText: {
+            readonly description: "A text value emitted as a workflow-visible scalar output.";
+            readonly examples: readonly [{
+                readonly name: "message";
+                readonly type: "text";
+            }];
+            readonly properties: {
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "If true, the output will not be shown in the history.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history.";
+                    readonly title: "Label";
+                };
+                readonly name: {
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                    readonly type: "string";
+                };
+                readonly type: {
+                    readonly const: "text";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["name", "type"];
+            readonly title: "IncomingToolOutputText";
+            readonly type: "object";
+        };
+        readonly IncomingUserToolOutputCollection: {
+            readonly additionalProperties: false;
+            readonly description: "A user-defined tool collection populated only by matching produced filenames.";
+            readonly examples: readonly [{
+                readonly collection_type: "list";
+                readonly discover_datasets: readonly [{
+                    readonly format: "txt";
+                    readonly pattern: "(?P<name>.+)\\.txt";
+                }];
+                readonly label: "Results";
+                readonly name: "results";
+                readonly type: "collection";
+            }];
+            readonly properties: {
+                readonly collection_type: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Fixed structure Galaxy creates for this output, such as `list`, `paired`, or a nested type such as `list:paired`.";
+                    readonly title: "Collection Type";
+                };
+                readonly collection_type_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Declared data-collection input whose runtime structure determines this output's collection type.";
+                    readonly title: "Collection Type Source";
+                };
+                readonly discover_datasets: {
+                    readonly anyOf: readonly [{
+                        readonly items: {
+                            readonly $ref: "#/$defs/FilePatternDatasetCollectionDescription";
+                        };
+                        readonly type: "array";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Filename pattern used to discover and populate collection elements.";
+                    readonly title: "Discover Datasets";
+                };
+                readonly format: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Default datatype extension assigned to collection elements.";
+                    readonly title: "Format";
+                };
+                readonly format_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Input whose datatype supplies the default format for collection elements.";
+                    readonly title: "Format Source";
+                };
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Hide the output in the history. The dataset is still created and usable by other tools and workflows.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly maxLength: 250;
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history. `$(inputs.<name>)` and `$(runtime.on_string)` references are filled in when the job is created.";
+                    readonly title: "Label";
+                };
+                readonly metadata_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Dataset input whose metadata supplies defaults for collection elements.";
+                    readonly title: "Metadata Source";
+                };
+                readonly name: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                };
+                readonly structured_like: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Declared input whose element count, identifiers, and nesting this output mirrors. Use this when each produced element corresponds to an input element.";
+                    readonly title: "Structured Like";
+                };
+                readonly type: {
+                    readonly const: "collection";
+                    readonly description: "Creates one history dataset collection populated from files produced by the command.";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["type"];
+            readonly title: "IncomingUserToolOutputCollection";
+            readonly type: "object";
+            readonly "x-usage-examples": readonly [{
+                readonly definition: {
+                    readonly inputs: readonly [];
+                    readonly outputs: readonly [{
+                        readonly collection_type: "list";
+                        readonly discover_datasets: readonly [{
+                            readonly directory: "reports";
+                            readonly format: "tabular";
+                            readonly pattern: "(?P<name>.+)\\.tsv";
+                        }];
+                        readonly name: "reports";
+                        readonly type: "collection";
+                    }];
+                    readonly shell_command: "mkdir reports && printf 'sample\\tvalue\\nA\\t1\\n' > reports/A.tsv && printf 'sample\\tvalue\\nB\\t2\\n' > reports/B.tsv";
+                };
+                readonly description: "`collection_type` can be used to declare a fixed output structure. A `list` contains an ordered set of discovered elements; `paired` requires `forward` and `reverse` identifiers.";
+                readonly field: "collection_type";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly collection_type: "paired";
+                        readonly format: readonly ["fastqsanger"];
+                        readonly name: "reads";
+                        readonly type: "data_collection";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly collection_type_source: "reads";
+                        readonly discover_datasets: readonly [{
+                            readonly directory: "copied";
+                            readonly format: "fastqsanger";
+                            readonly pattern: "(?P<name>forward|reverse)\\.fastq";
+                        }];
+                        readonly name: "copied_reads";
+                        readonly type: "collection";
+                    }];
+                    readonly shell_command: "mkdir copied && cp '$(inputs.reads.elements.forward.path)' copied/forward.fastq && cp '$(inputs.reads.elements.reverse.path)' copied/reverse.fastq";
+                };
+                readonly description: "`collection_type_source` can be used when the output has the same runtime collection type as a declared data-collection input, including when that input accepts more than one structure.";
+                readonly field: "collection_type_source";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly collection_type: "paired";
+                        readonly format: readonly ["fastqsanger"];
+                        readonly name: "reads";
+                        readonly type: "data_collection";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly collection_type: "paired";
+                        readonly discover_datasets: readonly [{
+                            readonly directory: "trimmed";
+                            readonly format: "fastqsanger";
+                            readonly pattern: "(?P<name>forward|reverse)\\.fastq";
+                        }];
+                        readonly name: "trimmed_reads";
+                        readonly structured_like: "reads";
+                        readonly type: "collection";
+                    }];
+                    readonly shell_command: "mkdir trimmed && head -n 400 '$(inputs.reads.elements.forward.path)' > trimmed/forward.fastq && head -n 400 '$(inputs.reads.elements.reverse.path)' > trimmed/reverse.fastq";
+                };
+                readonly description: "`structured_like` can be used when each produced element corresponds to an element of a declared input. Galaxy mirrors that input's element identifiers and nesting in the output.";
+                readonly field: "structured_like";
+            }];
+        };
+        readonly IncomingUserToolOutputDataset: {
+            readonly additionalProperties: false;
+            readonly description: "A user-defined tool dataset discovered only from files inside the job working directory.";
+            readonly examples: readonly [{
+                readonly format: "txt";
+                readonly from_work_dir: "result.txt";
+                readonly label: "Result";
+                readonly name: "result";
+                readonly type: "data";
+            }];
+            readonly properties: {
+                readonly discover_datasets: {
+                    readonly anyOf: readonly [{
+                        readonly items: {
+                            readonly $ref: "#/$defs/FilePatternDatasetCollectionDescription";
+                        };
+                        readonly type: "array";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Filename pattern used to discover additional datasets produced by the command.";
+                    readonly title: "Discover Datasets";
+                };
+                readonly format: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Galaxy datatype extension assigned when the command always produces a fixed representation. Use `format_source` instead when the datatype depends on an input.";
+                    readonly title: "Format";
+                };
+                readonly format_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Data or collection input whose datatype extension this output inherits. Use this when the command preserves the input representation, such as filtering reads without changing their format.";
+                    readonly title: "Format Source";
+                };
+                readonly from_work_dir: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Relative path, inside the job working directory, that the command writes for this output. Galaxy claims that file after the command finishes.";
+                    readonly title: "from_work_dir";
+                };
+                readonly hidden: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Hide the output in the history. The dataset is still created and usable by other tools and workflows.";
+                    readonly title: "Hidden";
+                };
+                readonly label: {
+                    readonly anyOf: readonly [{
+                        readonly maxLength: 250;
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Name shown for the produced dataset or collection in the history. `$(inputs.<name>)` and `$(runtime.on_string)` references are filled in when the job is created.";
+                    readonly title: "Label";
+                };
+                readonly metadata_source: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Data input whose datatype-specific metadata this output copies as defaults. Use this when the command preserves metadata Galaxy cannot infer from the output, such as interval column assignments.";
+                    readonly title: "Metadata Source";
+                };
+                readonly name: {
+                    readonly anyOf: readonly [{
+                        readonly type: "string";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly description: "Identifier used to connect this output in workflows and address it in tool tests.";
+                    readonly title: "Name";
+                };
+                readonly precreate_directory: {
+                    readonly anyOf: readonly [{
+                        readonly type: "boolean";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: false;
+                    readonly description: "Set true when `from_work_dir` names a produced directory for a composite datatype. Galaxy copies the directory contents into the output dataset's extra-files area.";
+                    readonly title: "Precreate Directory";
+                };
+                readonly type: {
+                    readonly const: "data";
+                    readonly description: "Creates one history dataset from a file produced by the command.";
+                    readonly title: "Type";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["type"];
+            readonly title: "IncomingUserToolOutputDataset";
+            readonly type: "object";
+            readonly "x-usage-examples": readonly [{
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly format: readonly ["fastqsanger"];
+                        readonly name: "reads";
+                        readonly type: "data";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly format: "fastqsanger";
+                        readonly from_work_dir: "first.fastq";
+                        readonly label: "$(inputs.reads.element_identifier) (first 400 lines)";
+                        readonly name: "first_reads";
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "head -n 400 '$(inputs.reads.path)' > first.fastq";
+                };
+                readonly description: "`label` can be used to name the output after the run's inputs. When the run maps over a collection, `$(inputs.reads.element_identifier)` is the sample name. [Output labels](#output-labels) lists the references a label can use.";
+                readonly field: "label";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [];
+                    readonly outputs: readonly [{
+                        readonly format: "tabular";
+                        readonly from_work_dir: "scores.tsv";
+                        readonly name: "scores";
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "printf 'gene\\tscore\\nBRCA1\\t0.95\\n' > scores.tsv";
+                };
+                readonly description: "`format` can be used to assign a fixed Galaxy datatype when every run writes the same representation. The value is a datatype extension, not a filename suffix.";
+                readonly field: "format";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly format: readonly ["fastq", "fastqsanger"];
+                        readonly name: "reads";
+                        readonly type: "data";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly format_source: "reads";
+                        readonly from_work_dir: "first.fastq";
+                        readonly name: "first_reads";
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "head -n 400 '$(inputs.reads.path)' > first.fastq";
+                };
+                readonly description: "`format_source` can be used to assign an output the selected input dataset's datatype when the command preserves its representation.";
+                readonly field: "format_source";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly format: readonly ["interval"];
+                        readonly name: "intervals";
+                        readonly type: "data";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly format: "interval";
+                        readonly from_work_dir: "filtered.interval";
+                        readonly metadata_source: "intervals";
+                        readonly name: "filtered_intervals";
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "awk '$3 > $2' '$(inputs.intervals.path)' > filtered.interval";
+                };
+                readonly description: "`metadata_source` can be used to copy datatype-specific metadata from an input when the command preserves information Galaxy cannot infer from the produced file, such as interval column assignments.";
+                readonly field: "metadata_source";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly label: "Message";
+                        readonly name: "message";
+                        readonly type: "text";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly format: "txt";
+                        readonly from_work_dir: "message.txt";
+                        readonly name: "message_file";
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "printf '%s\\n' '$(inputs.message)' > message.txt";
+                };
+                readonly description: "`from_work_dir` can be used to claim a file written by the command. The relative path must match the command's destination and remain inside the job working directory.";
+                readonly field: "from_work_dir";
+            }, {
+                readonly definition: {
+                    readonly inputs: readonly [{
+                        readonly format: readonly ["fasta"];
+                        readonly name: "reference";
+                        readonly type: "data";
+                    }];
+                    readonly outputs: readonly [{
+                        readonly format: "bwa_mem2_index";
+                        readonly from_work_dir: "index";
+                        readonly name: "index";
+                        readonly precreate_directory: true;
+                        readonly type: "data";
+                    }];
+                    readonly shell_command: "mkdir index && bwa-mem2 index -p index/reference '$(inputs.reference.path)'";
+                };
+                readonly description: "`precreate_directory` can be used with a directory-backed composite datatype. The command creates the directory named by `from_work_dir`; Galaxy then copies its contents into the output dataset's extra-files area.";
+                readonly field: "precreate_directory";
+            }];
+        };
         readonly JavascriptRequirement: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly expression_lib: {
                     readonly anyOf: readonly [{
                         readonly items: {
-                            readonly description: "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.";
+                            readonly description: "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside `shell_command` and `configfiles[*].content`.";
                             readonly examples: readonly ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"];
                             readonly title: "expression_lib";
                             readonly type: "string";
@@ -417,9 +1160,16 @@ export declare const userToolSourceSchema: {
         };
         readonly LengthParameterValidatorModel: {
             readonly additionalProperties: false;
+            readonly description: "Require the number of characters in a text value to fall within optional bounds.";
+            readonly examples: readonly [{
+                readonly max: 20;
+                readonly min: 1;
+                readonly type: "length";
+            }];
             readonly properties: {
                 readonly implicit: {
                     readonly default: false;
+                    readonly description: "Set internally when Galaxy added the validator automatically; tool authors normally leave this false.";
                     readonly title: "Implicit";
                     readonly type: "boolean";
                 };
@@ -430,6 +1180,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects text with more characters; omit to leave the length without an upper bound.";
                     readonly title: "Max";
                 };
                 readonly message: {
@@ -439,6 +1190,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Error message shown when validation fails; `%s` is replaced with the rejected value.";
                     readonly title: "Message";
                 };
                 readonly min: {
@@ -448,28 +1200,63 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects text with fewer characters; omit to leave the length without a lower bound.";
                     readonly title: "Min";
                 };
                 readonly negate: {
                     readonly default: false;
+                    readonly description: "Reject values whose length is inside the configured range instead of outside it.";
                     readonly title: "Negate";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "length";
                     readonly default: "length";
+                    readonly description: "Enforces character-count boundaries on a submitted text value.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
             };
             readonly title: "LengthParameterValidatorModel";
             readonly type: "object";
+            readonly "x-parameter-example": {
+                readonly label: "Sample name";
+                readonly name: "sample_name";
+                readonly type: "text";
+                readonly validators: readonly [{
+                    readonly max: 20;
+                    readonly min: 1;
+                    readonly type: "length";
+                }];
+            };
+        };
+        readonly MarkdownHelpContent: {
+            readonly additionalProperties: false;
+            readonly properties: {
+                readonly content: {
+                    readonly title: "Content";
+                    readonly type: "string";
+                };
+                readonly format: {
+                    readonly const: "markdown";
+                    readonly title: "Format";
+                    readonly type: "string";
+                };
+            };
+            readonly required: readonly ["format", "content"];
+            readonly title: "MarkdownHelpContent";
+            readonly type: "object";
         };
         readonly NoOptionsParameterValidatorModel: {
             readonly additionalProperties: false;
+            readonly description: "Require a select parameter to have at least one available option.";
+            readonly examples: readonly [{
+                readonly type: "no_options";
+            }];
             readonly properties: {
                 readonly implicit: {
                     readonly default: false;
+                    readonly description: "Set internally when Galaxy added the validator automatically; tool authors normally leave this false.";
                     readonly title: "Implicit";
                     readonly type: "boolean";
                 };
@@ -480,22 +1267,37 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Error message shown when validation fails; `%s` is replaced with the rejected value.";
                     readonly title: "Message";
                 };
                 readonly negate: {
                     readonly default: false;
+                    readonly description: "Require the select parameter to have no available options instead.";
                     readonly title: "Negate";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "no_options";
                     readonly default: "no_options";
+                    readonly description: "Fails validation when a select input has no choices available.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
             };
             readonly title: "NoOptionsParameterValidatorModel";
             readonly type: "object";
+            readonly "x-parameter-example": {
+                readonly label: "Reference database";
+                readonly name: "database";
+                readonly options: readonly [{
+                    readonly label: "Human";
+                    readonly value: "human";
+                }];
+                readonly type: "select";
+                readonly validators: readonly [{
+                    readonly type: "no_options";
+                }];
+            };
         };
         readonly OutputCompareType: {
             readonly enum: readonly ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"];
@@ -504,14 +1306,20 @@ export declare const userToolSourceSchema: {
         };
         readonly RegexParameterValidatorModel: {
             readonly additionalProperties: false;
-            readonly description: "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.";
+            readonly description: "Require a regular expression to match from the start of the value.\n\nEnd the expression with ``$`` to require a full-value match. Each option of\na select parameter is checked separately.";
+            readonly examples: readonly [{
+                readonly expression: "^[ACGT]+$";
+                readonly type: "regex";
+            }];
             readonly properties: {
                 readonly expression: {
+                    readonly description: "Regular expression matched from the start of the value. Add `$` at the end to require a complete-value match.";
                     readonly title: "Expression";
                     readonly type: "string";
                 };
                 readonly implicit: {
                     readonly default: false;
+                    readonly description: "Set internally when Galaxy added the validator automatically; tool authors normally leave this false.";
                     readonly title: "Implicit";
                     readonly type: "boolean";
                 };
@@ -522,16 +1330,19 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Error message shown when validation fails; `%s` is replaced with the rejected value.";
                     readonly title: "Message";
                 };
                 readonly negate: {
                     readonly default: false;
+                    readonly description: "Reject matching values instead of values that do not match.";
                     readonly title: "Negate";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "regex";
                     readonly default: "regex";
+                    readonly description: "Applies the regular expression in `expression` to each submitted text value.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -539,14 +1350,27 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["expression"];
             readonly title: "RegexParameterValidatorModel";
             readonly type: "object";
+            readonly "x-parameter-example": {
+                readonly label: "DNA motif";
+                readonly name: "motif";
+                readonly type: "text";
+                readonly validators: readonly [{
+                    readonly expression: "^[ACGT]+$";
+                    readonly type: "regex";
+                }];
+            };
         };
         readonly ResourceRequirement: {
+            readonly additionalProperties: false;
+            readonly description: "A tool's compute resource request.\n\nSet the minimum resources needed to run the job and, when useful, an upper\nlimit. Galaxy exposes the allocated CPU count to the command as\n``$GALAXY_SLOTS``. Use numbers or numeric strings. Other strings are\nreserved for expressions, which are not supported yet: a non-numeric value\nfails the create-time lint check.";
             readonly properties: {
                 readonly cores_max: {
                     readonly anyOf: readonly [{
                         readonly type: "integer";
                     }, {
                         readonly type: "number";
+                    }, {
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
@@ -559,6 +1383,8 @@ export declare const userToolSourceSchema: {
                         readonly type: "integer";
                     }, {
                         readonly type: "number";
+                    }, {
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
@@ -568,57 +1394,72 @@ export declare const userToolSourceSchema: {
                 };
                 readonly cuda_compute_capability: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Minimum CUDA compute capability required, e.g. 7.5.";
                     readonly title: "Cuda Compute Capability";
                 };
                 readonly cuda_device_count_max: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Maximum number of GPUs to reserve.";
                     readonly title: "Cuda Device Count Max";
                 };
                 readonly cuda_device_count_min: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Minimum number of GPUs to reserve.";
                     readonly title: "Cuda Device Count Min";
                 };
                 readonly cuda_version_min: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Minimum CUDA runtime version required, e.g. 11.2.";
                     readonly title: "Cuda Version Min";
                 };
                 readonly gpu_memory_min: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Minimum GPU memory required, in mebibytes (2**20).";
                     readonly title: "Gpu Memory Min";
                 };
                 readonly ram_max: {
@@ -626,6 +1467,8 @@ export declare const userToolSourceSchema: {
                         readonly type: "integer";
                     }, {
                         readonly type: "number";
+                    }, {
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
@@ -638,6 +1481,8 @@ export declare const userToolSourceSchema: {
                         readonly type: "integer";
                     }, {
                         readonly type: "number";
+                    }, {
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
@@ -647,13 +1492,16 @@ export declare const userToolSourceSchema: {
                 };
                 readonly shm_size: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Size of /dev/shm to request, in bytes.";
                     readonly title: "Shm Size";
                 };
                 readonly timelimit: {
@@ -661,6 +1509,8 @@ export declare const userToolSourceSchema: {
                         readonly type: "integer";
                     }, {
                         readonly type: "number";
+                    }, {
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
@@ -670,24 +1520,30 @@ export declare const userToolSourceSchema: {
                 };
                 readonly tmpdir_max: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Maximum reserved temporary directory space, in mebibytes (2**20).";
                     readonly title: "Tmpdir Max";
                 };
                 readonly tmpdir_min: {
                     readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
                         readonly type: "number";
                     }, {
-                        readonly type: "integer";
+                        readonly type: "string";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Minimum reserved temporary directory space, in mebibytes (2**20).";
                     readonly title: "Tmpdir Min";
                 };
                 readonly type: {
@@ -713,6 +1569,15 @@ export declare const userToolSourceSchema: {
                     readonly default: "Collection";
                     readonly title: "Class";
                 };
+                readonly count: {
+                    readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly title: "Count";
+                };
                 readonly element_tests: {
                     readonly anyOf: readonly [{
                         readonly additionalProperties: {
@@ -745,6 +1610,24 @@ export declare const userToolSourceSchema: {
                     readonly default: null;
                     readonly title: "Elements";
                 };
+                readonly max: {
+                    readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly title: "Maximum Count";
+                };
+                readonly min: {
+                    readonly anyOf: readonly [{
+                        readonly type: "integer";
+                    }, {
+                        readonly type: "null";
+                    }];
+                    readonly default: null;
+                    readonly title: "Minimum Count";
+                };
             };
             readonly title: "TestCollectionCollectionElementAssertions";
             readonly type: "object";
@@ -1129,187 +2012,12 @@ export declare const userToolSourceSchema: {
             readonly title: "TestDataOutputAssertions";
             readonly type: "object";
         };
-        readonly ToolOutputBoolean: {
-            readonly properties: {
-                readonly hidden: {
-                    readonly description: "If true, the output will not be shown in the history.";
-                    readonly title: "Hidden";
-                };
-                readonly label: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
-                    readonly title: "Label";
-                };
-                readonly name: {
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
-                    readonly title: "Name";
-                };
-                readonly type: {
-                    readonly const: "boolean";
-                    readonly title: "Type";
-                    readonly type: "string";
-                };
-            };
-            readonly required: readonly ["name", "hidden", "type"];
-            readonly title: "ToolOutputBoolean";
-            readonly type: "object";
-        };
-        readonly ToolOutputCollectionStructure: {
-            readonly properties: {
-                readonly collection_type: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Collection Type";
-                };
-                readonly collection_type_from_rules: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Collection Type From Rules";
-                };
-                readonly collection_type_source: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Collection Type Source";
-                };
-                readonly discover_datasets: {
-                    readonly anyOf: readonly [{
-                        readonly items: {
-                            readonly anyOf: readonly [{
-                                readonly $ref: "#/$defs/FilePatternDatasetCollectionDescription";
-                            }, {
-                                readonly $ref: "#/$defs/ToolProvidedMetadataDatasetCollection";
-                            }];
-                        };
-                        readonly type: "array";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Discover Datasets";
-                };
-                readonly structured_like: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Structured Like";
-                };
-            };
-            readonly title: "ToolOutputCollectionStructure";
-            readonly type: "object";
-        };
-        readonly ToolOutputFloat: {
-            readonly properties: {
-                readonly hidden: {
-                    readonly description: "If true, the output will not be shown in the history.";
-                    readonly title: "Hidden";
-                };
-                readonly label: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
-                    readonly title: "Label";
-                };
-                readonly name: {
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
-                    readonly title: "Name";
-                };
-                readonly type: {
-                    readonly const: "float";
-                    readonly title: "Type";
-                    readonly type: "string";
-                };
-            };
-            readonly required: readonly ["name", "hidden", "type"];
-            readonly title: "ToolOutputFloat";
-            readonly type: "object";
-        };
-        readonly ToolOutputInteger: {
-            readonly properties: {
-                readonly hidden: {
-                    readonly description: "If true, the output will not be shown in the history.";
-                    readonly title: "Hidden";
-                };
-                readonly label: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
-                    readonly title: "Label";
-                };
-                readonly name: {
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
-                    readonly title: "Name";
-                };
-                readonly type: {
-                    readonly const: "integer";
-                    readonly title: "Type";
-                    readonly type: "string";
-                };
-            };
-            readonly required: readonly ["name", "hidden", "type"];
-            readonly title: "ToolOutputInteger";
-            readonly type: "object";
-        };
-        readonly ToolOutputText: {
-            readonly properties: {
-                readonly hidden: {
-                    readonly description: "If true, the output will not be shown in the history.";
-                    readonly title: "Hidden";
-                };
-                readonly label: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly description: "Output label. Will be used as dataset name in history.";
-                    readonly title: "Label";
-                };
-                readonly name: {
-                    readonly description: "Parameter name. Used when referencing parameter in workflows.";
-                    readonly title: "Name";
-                };
-                readonly type: {
-                    readonly const: "text";
-                    readonly title: "Type";
-                    readonly type: "string";
-                };
-            };
-            readonly required: readonly ["name", "hidden", "type"];
-            readonly title: "ToolOutputText";
-            readonly type: "object";
-        };
         readonly ToolProvidedMetadataDatasetCollection: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly assign_primary_output: {
+                    readonly default: false;
+                    readonly description: "Whether the first matching file replaces the primary dataset output.";
                     readonly title: "Assign Primary Output";
                     readonly type: "boolean";
                 };
@@ -1319,10 +2027,13 @@ export declare const userToolSourceSchema: {
                     }, {
                         readonly type: "null";
                     }];
+                    readonly default: null;
+                    readonly description: "Directory to search, relative to the job working directory.";
                     readonly title: "Directory";
                 };
                 readonly discover_via: {
                     readonly const: "tool_provided_metadata";
+                    readonly description: "Read discovered dataset details from the tool-provided metadata file.";
                     readonly title: "Discover Via";
                     readonly type: "string";
                 };
@@ -1332,27 +2043,56 @@ export declare const userToolSourceSchema: {
                     }, {
                         readonly type: "null";
                     }];
+                    readonly default: null;
+                    readonly description: "Galaxy datatype extension assigned to each discovered dataset.";
                     readonly title: "Format";
                 };
                 readonly match_relative_path: {
+                    readonly default: false;
+                    readonly description: "Whether `pattern` matches each file's relative path instead of only its filename.";
                     readonly title: "Match Relative Path";
                     readonly type: "boolean";
                 };
                 readonly recurse: {
+                    readonly default: false;
+                    readonly description: "Whether to search recursively below `directory`.";
                     readonly title: "Recurse";
                     readonly type: "boolean";
                 };
                 readonly visible: {
+                    readonly default: false;
+                    readonly description: "Whether discovered datasets are visible in the history.";
                     readonly title: "Visible";
                     readonly type: "boolean";
                 };
             };
-            readonly required: readonly ["discover_via", "format", "visible", "assign_primary_output", "directory", "recurse", "match_relative_path"];
+            readonly required: readonly ["discover_via"];
             readonly title: "ToolProvidedMetadataDatasetCollection";
             readonly type: "object";
         };
         readonly UserToolSource: {
             readonly additionalProperties: false;
+            readonly description: "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.";
+            readonly examples: readonly [{
+                readonly class: "GalaxyUserTool";
+                readonly container: "quay.io/biocontainers/grep:3.4--hf43ccf4_4";
+                readonly description: "from a text file";
+                readonly id: "remove_comments";
+                readonly inputs: readonly [{
+                    readonly format: readonly ["txt"];
+                    readonly name: "input_file";
+                    readonly type: "data";
+                }];
+                readonly name: "Remove Comment Lines";
+                readonly outputs: readonly [{
+                    readonly format_source: "input_file";
+                    readonly from_work_dir: "output.txt";
+                    readonly name: "output_file";
+                    readonly type: "data";
+                }];
+                readonly shell_command: "grep -v '^#' '$(inputs.input_file.path)' > output.txt || test \"$?\" = 1";
+                readonly version: "0.1.0";
+            }];
             readonly properties: {
                 readonly citations: {
                     readonly anyOf: readonly [{
@@ -1364,6 +2104,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "DOI or BibTeX references for publications describing the wrapped tool.";
                     readonly title: "citations";
                 };
                 readonly class: {
@@ -1381,11 +2122,11 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "A list of config files for this tool.";
+                    readonly description: "Files Galaxy writes into the job working directory before running the command. Their content is evaluated with the same sandboxed ECMAScript expressions as `shell_command`. Put scripts and other substantial command logic here, then keep `shell_command` to a short invocation.";
                     readonly title: "configfiles";
                 };
                 readonly container: {
-                    readonly description: "Container image to use for this tool.";
+                    readonly description: "Docker container image for the tool, as a fully qualified registry/repository:tag string. This image is the tool's entire execution environment, so every command used by shell_command must already exist in it. Do not prefix the value with 'docker://' -- Galaxy adds that itself for Singularity and Apptainer destinations. An unqualified name is resolved against the container runtime's own default registry (Docker Hub), which is rarely what you want.";
                     readonly examples: readonly ["quay.io/biocontainers/python:3.13"];
                     readonly title: "container";
                     readonly type: "string";
@@ -1410,6 +2151,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "EDAM operation identifiers such as `operation_0308`.";
                     readonly title: "edam_operations";
                 };
                 readonly edam_topics: {
@@ -1422,16 +2164,17 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "EDAM topic identifiers such as `topic_0102`.";
                     readonly title: "edam_topics";
                 };
                 readonly help: {
                     readonly anyOf: readonly [{
-                        readonly $ref: "#/$defs/HelpContent";
+                        readonly $ref: "#/$defs/MarkdownHelpContent";
                     }, {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Help text shown below the tool interface.";
+                    readonly description: "Help shown below the tool form. Set `format` to `markdown` and put the documentation in `content`.";
                     readonly title: "help";
                 };
                 readonly id: {
@@ -1450,6 +2193,7 @@ export declare const userToolSourceSchema: {
                 };
                 readonly inputs: {
                     readonly default: readonly [];
+                    readonly description: "Parameters displayed on the tool form. Each item needs a unique `name` and a supported `type`. Reference scalar values as `$(inputs.input_name)` and data inputs as `$(inputs.input_name.path)` in `shell_command` or config files. Conditional, repeat, and section inputs contain nested parameters.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlGalaxyToolParameter";
                     };
@@ -1475,30 +2219,19 @@ export declare const userToolSourceSchema: {
                 };
                 readonly outputs: {
                     readonly default: readonly [];
+                    readonly description: "Datasets and dataset collections Galaxy collects after the command finishes. A data output identifies its produced file with `from_work_dir` or `discover_datasets`; a collection output uses `discover_datasets`.";
                     readonly items: {
                         readonly discriminator: {
                             readonly mapping: {
-                                readonly boolean: "#/$defs/ToolOutputBoolean";
-                                readonly collection: "#/$defs/IncomingToolOutputCollection";
-                                readonly data: "#/$defs/IncomingToolOutputDataset";
-                                readonly float: "#/$defs/ToolOutputFloat";
-                                readonly integer: "#/$defs/ToolOutputInteger";
-                                readonly text: "#/$defs/ToolOutputText";
+                                readonly collection: "#/$defs/IncomingUserToolOutputCollection";
+                                readonly data: "#/$defs/IncomingUserToolOutputDataset";
                             };
                             readonly propertyName: "type";
                         };
                         readonly oneOf: readonly [{
-                            readonly $ref: "#/$defs/IncomingToolOutputDataset";
-                        }, {
-                            readonly $ref: "#/$defs/IncomingToolOutputCollection";
+                            readonly $ref: "#/$defs/IncomingUserToolOutputDataset";
                         }, {
-                            readonly $ref: "#/$defs/ToolOutputText";
-                        }, {
-                            readonly $ref: "#/$defs/ToolOutputInteger";
-                        }, {
-                            readonly $ref: "#/$defs/ToolOutputFloat";
-                        }, {
-                            readonly $ref: "#/$defs/ToolOutputBoolean";
+                            readonly $ref: "#/$defs/IncomingUserToolOutputCollection";
                         }];
                     };
                     readonly title: "outputs";
@@ -1520,8 +2253,6 @@ export declare const userToolSourceSchema: {
                                 readonly $ref: "#/$defs/JavascriptRequirement";
                             }, {
                                 readonly $ref: "#/$defs/ResourceRequirement";
-                            }, {
-                                readonly $ref: "#/$defs/ContainerRequirement";
                             }];
                         };
                         readonly type: "array";
@@ -1529,12 +2260,12 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: readonly [];
-                    readonly description: "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.";
+                    readonly description: "JavaScript helpers and compute resource requests needed to execute this tool.";
                     readonly title: "requirements";
                 };
                 readonly shell_command: {
-                    readonly description: "A string that contains the command to be executed. Parameters can be referenced inside $().";
-                    readonly examples: readonly ["head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'"];
+                    readonly description: "A string that contains the command to be executed. Reference inputs inside `$()` as `$(inputs.input_name)` for scalar values and `$(inputs.input_name.path)` for files; `${ ... }` evaluates a JavaScript function body that must return a value. Substituted values are not shell-quoted, so quote them yourself. Because `$(` and `${` are consumed by the expression evaluator, shell command substitution and braced parameter expansion do not reach the shell: escape them as `\\$(` and `\\${`, and prefer unbraced variables such as `$GALAXY_SLOTS`.";
+                    readonly examples: readonly ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"];
                     readonly title: "shell_command";
                     readonly type: "string";
                 };
@@ -1548,18 +2279,14 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Tool test declarations with input values and expected outputs. Database-stored user-defined tools retain these declarations but do not currently run them in the application.";
                     readonly title: "tests";
                 };
                 readonly version: {
-                    readonly anyOf: readonly [{
-                        readonly type: "string";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
                     readonly description: "Version for the tool.";
                     readonly examples: readonly ["0.1.0"];
                     readonly title: "version";
+                    readonly type: "string";
                 };
                 readonly xrefs: {
                     readonly anyOf: readonly [{
@@ -1571,12 +2298,14 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "External registry identifiers, each with a registry `type` and identifier `value`.";
                     readonly title: "xrefs";
                 };
             };
-            readonly required: readonly ["name", "shell_command", "class", "container"];
+            readonly required: readonly ["version", "name", "shell_command", "class", "container"];
             readonly title: "UserToolSource";
             readonly type: "object";
+            readonly "x-field-order": readonly ["class", "id", "name", "version", "description", "container", "requirements", "shell_command", "configfiles", "inputs", "outputs", "citations", "license", "profile", "edam_operations", "edam_topics", "xrefs", "help", "tests"];
         };
         readonly XrefDict: {
             readonly additionalProperties: false;
@@ -1596,6 +2325,13 @@ export declare const userToolSourceSchema: {
         };
         readonly YamlBooleanParameter: {
             readonly additionalProperties: false;
+            readonly description: "A true-or-false input.";
+            readonly examples: readonly [{
+                readonly label: "Include a header line";
+                readonly name: "include_header";
+                readonly type: "boolean";
+                readonly value: true;
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -1604,6 +2340,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1613,19 +2350,23 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "boolean";
+                    readonly description: "Presents a true-or-false choice and supplies the selected Boolean value to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -1636,15 +2377,24 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: false;
+                    readonly description: "Initial choice shown when the user first opens the tool form.";
                     readonly title: "Value";
                 };
             };
             readonly required: readonly ["name", "type"];
             readonly title: "YamlBooleanParameter";
             readonly type: "object";
+            readonly "x-shell-command": "include_header=\"$(inputs.include_header)\"";
         };
         readonly YamlColorParameter: {
             readonly additionalProperties: false;
+            readonly description: "A color-picker input.";
+            readonly examples: readonly [{
+                readonly label: "Plot color";
+                readonly name: "plot_color";
+                readonly type: "color";
+                readonly value: "#3366cc";
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -1653,6 +2403,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1662,19 +2413,23 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "color";
+                    readonly description: "Presents a color picker and supplies the selected hexadecimal color string.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -1685,15 +2440,47 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Color initially selected in the picker, written in hexadecimal notation.";
                     readonly title: "Value";
                 };
             };
             readonly required: readonly ["name", "type"];
             readonly title: "YamlColorParameter";
             readonly type: "object";
+            readonly "x-shell-command": "plot_color=\"$(inputs.plot_color)\"";
         };
         readonly YamlConditionalParameter: {
             readonly additionalProperties: false;
+            readonly description: "A control input that selects which nested inputs are displayed and supplied to the command.";
+            readonly examples: readonly [{
+                readonly name: "search_options";
+                readonly test_parameter: {
+                    readonly label: "Search mode";
+                    readonly name: "mode";
+                    readonly options: readonly [{
+                        readonly label: "Fast";
+                        readonly selected: true;
+                        readonly value: "fast";
+                    }, {
+                        readonly label: "Sensitive";
+                        readonly selected: false;
+                        readonly value: "sensitive";
+                    }];
+                    readonly type: "select";
+                };
+                readonly type: "conditional";
+                readonly whens: readonly [{
+                    readonly discriminator: "fast";
+                    readonly parameters: readonly [];
+                }, {
+                    readonly discriminator: "sensitive";
+                    readonly parameters: readonly [{
+                        readonly name: "iterations";
+                        readonly type: "integer";
+                        readonly value: 3;
+                    }];
+                }];
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -1702,6 +2489,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1711,18 +2499,22 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly test_parameter: {
+                    readonly description: "Boolean or select input whose submitted value chooses the active `whens` branch.";
                     readonly discriminator: {
                         readonly mapping: {
                             readonly boolean: "#/$defs/YamlBooleanParameter";
@@ -1739,10 +2531,12 @@ export declare const userToolSourceSchema: {
                 };
                 readonly type: {
                     readonly const: "conditional";
+                    readonly description: "Shows one set of nested inputs at a time according to a Boolean or select control.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
                 readonly whens: {
+                    readonly description: "Maps each control value to the nested parameters shown and supplied for that branch.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlConditionalWhen";
                     };
@@ -1754,6 +2548,7 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type", "test_parameter", "whens"];
             readonly title: "YamlConditionalParameter";
             readonly type: "object";
+            readonly "x-shell-command": "mode=\"$(inputs.search_options.mode)\"\niterations=\"$(inputs.search_options.iterations)\"";
         };
         readonly YamlConditionalWhen: {
             readonly additionalProperties: false;
@@ -1781,6 +2576,14 @@ export declare const userToolSourceSchema: {
         };
         readonly YamlDataCollectionParameter: {
             readonly additionalProperties: false;
+            readonly description: "A dataset collection input.";
+            readonly examples: readonly [{
+                readonly collection_type: "paired";
+                readonly format: readonly ["fastqsanger"];
+                readonly label: "Paired reads";
+                readonly name: "reads";
+                readonly type: "data_collection";
+            }];
             readonly properties: {
                 readonly collection_type: {
                     readonly anyOf: readonly [{
@@ -1789,10 +2592,12 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Limits selectable collections to this structure, such as `list` or `paired`.";
                     readonly title: "Collection Type";
                 };
                 readonly format: {
                     readonly default: readonly ["data"];
+                    readonly description: "Requires every selectable collection element to use one of these datatype extensions.";
                     readonly items: {
                         readonly type: "string";
                     };
@@ -1806,6 +2611,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1815,19 +2621,23 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "data_collection";
+                    readonly description: "Lets the user select a history collection and exposes its elements to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -1835,12 +2645,21 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type"];
             readonly title: "YamlDataCollectionParameter";
             readonly type: "object";
+            readonly "x-shell-command": "forward='$(inputs.reads.elements.forward.path)'\nreverse='$(inputs.reads.elements.reverse.path)'";
         };
         readonly YamlDataParameter: {
             readonly additionalProperties: false;
+            readonly description: "One dataset, or a list of datasets when ``multiple`` is true.";
+            readonly examples: readonly [{
+                readonly format: readonly ["txt", "tabular"];
+                readonly label: "Input file";
+                readonly name: "input_file";
+                readonly type: "data";
+            }];
             readonly properties: {
                 readonly format: {
                     readonly default: readonly ["data"];
+                    readonly description: "Limits selectable datasets to these Galaxy datatype extensions.";
                     readonly items: {
                         readonly type: "string";
                     };
@@ -1854,6 +2673,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1863,42 +2683,29 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
-                readonly max: {
-                    readonly anyOf: readonly [{
-                        readonly type: "integer";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Max";
-                };
-                readonly min: {
-                    readonly anyOf: readonly [{
-                        readonly type: "integer";
-                    }, {
-                        readonly type: "null";
-                    }];
-                    readonly default: null;
-                    readonly title: "Min";
-                };
                 readonly multiple: {
                     readonly default: false;
+                    readonly description: "Set true to accept several datasets (a list) for this input instead of one.";
                     readonly title: "Multiple";
                     readonly type: "boolean";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "data";
+                    readonly description: "Lets the user select history datasets and exposes their paths and metadata to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -1906,9 +2713,19 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type"];
             readonly title: "YamlDataParameter";
             readonly type: "object";
+            readonly "x-shell-command": "input_file='$(inputs.input_file.path)'";
         };
         readonly YamlFloatParameter: {
             readonly additionalProperties: false;
+            readonly description: "A numeric input with optional bounds and validators.";
+            readonly examples: readonly [{
+                readonly label: "Score threshold";
+                readonly max: 1;
+                readonly min: 0;
+                readonly name: "threshold";
+                readonly type: "float";
+                readonly value: 0.5;
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -1917,6 +2734,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -1926,6 +2744,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly max: {
@@ -1935,6 +2754,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects submitted values larger than this inclusive upper bound.";
                     readonly title: "Max";
                 };
                 readonly min: {
@@ -1944,24 +2764,29 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects submitted values smaller than this inclusive lower bound.";
                     readonly title: "Min";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "float";
+                    readonly description: "Accepts a number, including decimal values, and supplies it to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
                 readonly validators: {
                     readonly default: readonly [];
+                    readonly description: "Additional validation rules; supports `in_range`.";
                     readonly items: {
                         readonly $ref: "#/$defs/InRangeParameterValidatorModel";
                     };
@@ -1975,12 +2800,14 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Number prefilled when the user first opens the tool form.";
                     readonly title: "Value";
                 };
             };
             readonly required: readonly ["name", "type"];
             readonly title: "YamlFloatParameter";
             readonly type: "object";
+            readonly "x-shell-command": "threshold=\"$(inputs.threshold)\"";
         };
         readonly YamlGalaxyToolParameter: {
             readonly discriminator: {
@@ -2026,6 +2853,15 @@ export declare const userToolSourceSchema: {
         };
         readonly YamlIntegerParameter: {
             readonly additionalProperties: false;
+            readonly description: "A whole-number input with optional bounds and validators.";
+            readonly examples: readonly [{
+                readonly label: "Number of lines";
+                readonly max: 1000;
+                readonly min: 1;
+                readonly name: "num_lines";
+                readonly type: "integer";
+                readonly value: 10;
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -2034,6 +2870,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -2043,6 +2880,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly max: {
@@ -2052,6 +2890,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects submitted values larger than this inclusive upper bound.";
                     readonly title: "Max";
                 };
                 readonly min: {
@@ -2061,24 +2900,29 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Rejects submitted values smaller than this inclusive lower bound.";
                     readonly title: "Min";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "integer";
+                    readonly description: "Accepts a whole number and supplies it as a numeric value to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
                 readonly validators: {
                     readonly default: readonly [];
+                    readonly description: "Additional validation rules; supports `in_range`.";
                     readonly items: {
                         readonly $ref: "#/$defs/InRangeParameterValidatorModel";
                     };
@@ -2092,14 +2936,17 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Number prefilled when the user first opens the tool form.";
                     readonly title: "Value";
                 };
             };
             readonly required: readonly ["name", "type"];
             readonly title: "YamlIntegerParameter";
             readonly type: "object";
+            readonly "x-shell-command": "num_lines=\"$(inputs.num_lines)\"";
         };
         readonly YamlLabelValue: {
+            readonly additionalProperties: false;
             readonly description: "YAML-friendly option model — ``selected`` defaults to ``False``.";
             readonly properties: {
                 readonly label: {
@@ -2122,6 +2969,19 @@ export declare const userToolSourceSchema: {
         };
         readonly YamlRepeatParameter: {
             readonly additionalProperties: false;
+            readonly description: "A group the user may add multiple times, with ``parameters`` defining one repeated entry.";
+            readonly examples: readonly [{
+                readonly label: "Additional files";
+                readonly max: 3;
+                readonly min: 0;
+                readonly name: "extra_files";
+                readonly parameters: readonly [{
+                    readonly format: readonly ["txt"];
+                    readonly name: "input_file";
+                    readonly type: "data";
+                }];
+                readonly type: "repeat";
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -2130,6 +2990,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -2139,6 +3000,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly max: {
@@ -2148,6 +3010,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Prevents the user from adding more than this many entries.";
                     readonly title: "Max";
                 };
                 readonly min: {
@@ -2157,19 +3020,23 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Keeps at least this many entries in the group and creates them when the form opens.";
                     readonly title: "Min";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly parameters: {
                     readonly default: readonly [];
+                    readonly description: "Nested inputs that make up one entry in the repeated group.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlGalaxyToolParameter";
                     };
@@ -2178,6 +3045,7 @@ export declare const userToolSourceSchema: {
                 };
                 readonly type: {
                     readonly const: "repeat";
+                    readonly description: "Lets the user add multiple entries that all contain the same nested inputs.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -2185,9 +3053,23 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type"];
             readonly title: "YamlRepeatParameter";
             readonly type: "object";
+            readonly "x-shell-command": "files='$(inputs.extra_files.map((item) => item.input_file.path).join(\" \"))'";
         };
         readonly YamlSectionParameter: {
             readonly additionalProperties: false;
+            readonly description: "Related inputs that users can expand or collapse to reduce form complexity.";
+            readonly examples: readonly [{
+                readonly label: "Advanced options";
+                readonly name: "advanced";
+                readonly parameters: readonly [{
+                    readonly max: 1;
+                    readonly min: 0;
+                    readonly name: "threshold";
+                    readonly type: "float";
+                    readonly value: 0.5;
+                }];
+                readonly type: "section";
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -2196,6 +3078,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -2205,19 +3088,23 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly parameters: {
                     readonly default: readonly [];
+                    readonly description: "Nested inputs displayed together inside the section.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlGalaxyToolParameter";
                     };
@@ -2226,6 +3113,7 @@ export declare const userToolSourceSchema: {
                 };
                 readonly type: {
                     readonly const: "section";
+                    readonly description: "Places related inputs in a collapsible group to simplify the tool form.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
@@ -2233,9 +3121,25 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type"];
             readonly title: "YamlSectionParameter";
             readonly type: "object";
+            readonly "x-shell-command": "threshold=\"$(inputs.advanced.threshold)\"";
         };
         readonly YamlSelectParameter: {
             readonly additionalProperties: false;
+            readonly description: "A choice from a fixed list of options.";
+            readonly examples: readonly [{
+                readonly label: "Search mode";
+                readonly name: "mode";
+                readonly options: readonly [{
+                    readonly label: "Fast";
+                    readonly selected: true;
+                    readonly value: "fast";
+                }, {
+                    readonly label: "Sensitive";
+                    readonly selected: false;
+                    readonly value: "sensitive";
+                }];
+                readonly type: "select";
+            }];
             readonly properties: {
                 readonly help: {
                     readonly anyOf: readonly [{
@@ -2244,6 +3148,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -2253,23 +3158,28 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly multiple: {
                     readonly default: false;
+                    readonly description: "Set true to let the user select and supply several option values instead of one.";
                     readonly title: "Multiple";
                     readonly type: "boolean";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly options: {
+                    readonly description: "Choices presented on the tool form, each with a display label and value.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlLabelValue";
                     };
@@ -2279,11 +3189,13 @@ export declare const userToolSourceSchema: {
                 };
                 readonly type: {
                     readonly const: "select";
+                    readonly description: "Lets the user choose from the declared `options` and supplies the selected value.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
                 readonly validators: {
                     readonly default: readonly [];
+                    readonly description: "Additional validation rules; supports `no_options`.";
                     readonly items: {
                         readonly $ref: "#/$defs/NoOptionsParameterValidatorModel";
                     };
@@ -2294,8 +3206,10 @@ export declare const userToolSourceSchema: {
             readonly required: readonly ["name", "type", "options"];
             readonly title: "YamlSelectParameter";
             readonly type: "object";
+            readonly "x-shell-command": "mode=\"$(inputs.mode)\"";
         };
         readonly YamlTemplateConfigFile: {
+            readonly additionalProperties: false;
             readonly properties: {
                 readonly content: {
                     readonly title: "Content";
@@ -2391,9 +3305,18 @@ export declare const userToolSourceSchema: {
         };
         readonly YamlTextParameter: {
             readonly additionalProperties: false;
+            readonly description: "A single-line or multiline text input.";
+            readonly examples: readonly [{
+                readonly area: false;
+                readonly label: "Sequence motif";
+                readonly name: "motif";
+                readonly type: "text";
+                readonly value: "ACGT";
+            }];
             readonly properties: {
                 readonly area: {
                     readonly default: false;
+                    readonly description: "Set true to use a multiline editor instead of a single-line text box.";
                     readonly title: "Area";
                     readonly type: "boolean";
                 };
@@ -2404,6 +3327,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Additional guidance shown on the tool form to help users choose a value.";
                     readonly title: "Help";
                 };
                 readonly label: {
@@ -2413,24 +3337,29 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Label shown for the input on the tool form.";
                     readonly title: "Label";
                 };
                 readonly name: {
+                    readonly description: "Identifier used to read this input from `shell_command` and other expressions.";
                     readonly title: "Name";
                     readonly type: "string";
                 };
                 readonly optional: {
                     readonly default: false;
+                    readonly description: "Set true when the command can run without the user supplying this input.";
                     readonly title: "Optional";
                     readonly type: "boolean";
                 };
                 readonly type: {
                     readonly const: "text";
+                    readonly description: "Accepts user-entered text and supplies the resulting string to expressions.";
                     readonly title: "Type";
                     readonly type: "string";
                 };
                 readonly validators: {
                     readonly default: readonly [];
+                    readonly description: "Additional validation rules; supports `length`, `regex`, and `empty_field`.";
                     readonly items: {
                         readonly anyOf: readonly [{
                             readonly $ref: "#/$defs/LengthParameterValidatorModel";
@@ -2450,12 +3379,14 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "Text prefilled when the user first opens the tool form.";
                     readonly title: "Value";
                 };
             };
             readonly required: readonly ["name", "type"];
             readonly title: "YamlTextParameter";
             readonly type: "object";
+            readonly "x-shell-command": "motif=\"$(inputs.motif)\"";
         };
         readonly YamlToolSource: {
             readonly additionalProperties: false;
@@ -2470,6 +3401,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "DOI or BibTeX references for publications describing the wrapped tool.";
                     readonly title: "citations";
                 };
                 readonly class: {
@@ -2487,7 +3419,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "A list of config files for this tool.";
+                    readonly description: "Files Galaxy writes into the job working directory before running the command. Their content is evaluated with the same sandboxed ECMAScript expressions as `shell_command`. Put scripts and other substantial command logic here, then keep `shell_command` to a short invocation.";
                     readonly title: "configfiles";
                 };
                 readonly container: {
@@ -2521,6 +3453,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "EDAM operation identifiers such as `operation_0308`.";
                     readonly title: "edam_operations";
                 };
                 readonly edam_topics: {
@@ -2533,6 +3466,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "EDAM topic identifiers such as `topic_0102`.";
                     readonly title: "edam_topics";
                 };
                 readonly help: {
@@ -2542,7 +3476,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
-                    readonly description: "Help text shown below the tool interface.";
+                    readonly description: "Help shown below the tool form. Set `format` to `markdown`, `restructuredtext`, or `plain_text`, and put the documentation in `content`.";
                     readonly title: "help";
                 };
                 readonly id: {
@@ -2561,6 +3495,7 @@ export declare const userToolSourceSchema: {
                 };
                 readonly inputs: {
                     readonly default: readonly [];
+                    readonly description: "Parameters displayed on the tool form. Each item needs a unique `name` and a supported `type`. Reference scalar values as `$(inputs.input_name)` and data inputs as `$(inputs.input_name.path)` in `shell_command` or config files. Conditional, repeat, and section inputs contain nested parameters.";
                     readonly items: {
                         readonly $ref: "#/$defs/YamlGalaxyToolParameter";
                     };
@@ -2586,15 +3521,16 @@ export declare const userToolSourceSchema: {
                 };
                 readonly outputs: {
                     readonly default: readonly [];
+                    readonly description: "Results Galaxy collects after the command finishes. A data output identifies its produced file with `from_work_dir` or `discover_datasets`; a collection output uses `discover_datasets`. Scalar output types are `text`, `integer`, `float`, and `boolean`.";
                     readonly items: {
                         readonly discriminator: {
                             readonly mapping: {
-                                readonly boolean: "#/$defs/ToolOutputBoolean";
+                                readonly boolean: "#/$defs/IncomingToolOutputBoolean";
                                 readonly collection: "#/$defs/IncomingToolOutputCollection";
                                 readonly data: "#/$defs/IncomingToolOutputDataset";
-                                readonly float: "#/$defs/ToolOutputFloat";
-                                readonly integer: "#/$defs/ToolOutputInteger";
-                                readonly text: "#/$defs/ToolOutputText";
+                                readonly float: "#/$defs/IncomingToolOutputFloat";
+                                readonly integer: "#/$defs/IncomingToolOutputInteger";
+                                readonly text: "#/$defs/IncomingToolOutputText";
                             };
                             readonly propertyName: "type";
                         };
@@ -2603,13 +3539,13 @@ export declare const userToolSourceSchema: {
                         }, {
                             readonly $ref: "#/$defs/IncomingToolOutputCollection";
                         }, {
-                            readonly $ref: "#/$defs/ToolOutputText";
+                            readonly $ref: "#/$defs/IncomingToolOutputText";
                         }, {
-                            readonly $ref: "#/$defs/ToolOutputInteger";
+                            readonly $ref: "#/$defs/IncomingToolOutputInteger";
                         }, {
-                            readonly $ref: "#/$defs/ToolOutputFloat";
+                            readonly $ref: "#/$defs/IncomingToolOutputFloat";
                         }, {
-                            readonly $ref: "#/$defs/ToolOutputBoolean";
+                            readonly $ref: "#/$defs/IncomingToolOutputBoolean";
                         }];
                     };
                     readonly title: "outputs";
@@ -2640,12 +3576,12 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: readonly [];
-                    readonly description: "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.";
+                    readonly description: "JavaScript helpers and compute resource requests needed to execute this tool.";
                     readonly title: "requirements";
                 };
                 readonly shell_command: {
-                    readonly description: "A string that contains the command to be executed. Parameters can be referenced inside $().";
-                    readonly examples: readonly ["head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'"];
+                    readonly description: "A string that contains the command to be executed. Reference inputs inside `$()` as `$(inputs.input_name)` for scalar values and `$(inputs.input_name.path)` for files; `${ ... }` evaluates a JavaScript function body that must return a value. Substituted values are not shell-quoted, so quote them yourself. Because `$(` and `${` are consumed by the expression evaluator, shell command substitution and braced parameter expansion do not reach the shell: escape them as `\\$(` and `\\${`, and prefer unbraced variables such as `$GALAXY_SLOTS`.";
+                    readonly examples: readonly ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"];
                     readonly title: "shell_command";
                     readonly type: "string";
                 };
@@ -2682,6 +3618,7 @@ export declare const userToolSourceSchema: {
                         readonly type: "null";
                     }];
                     readonly default: null;
+                    readonly description: "External registry identifiers, each with a registry `type` and identifier `value`.";
                     readonly title: "xrefs";
                 };
             };