@galaxy-tool-util/schema 1.2.0 → 1.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (96) hide show
  1. package/dist/index.d.ts +27 -1
  2. package/dist/index.d.ts.map +1 -1
  3. package/dist/index.js +27 -1
  4. package/dist/index.js.map +1 -1
  5. package/dist/schema/parsed-tool.d.ts +3 -0
  6. package/dist/schema/parsed-tool.d.ts.map +1 -1
  7. package/dist/user-tool-parse/index.d.ts +12 -0
  8. package/dist/user-tool-parse/index.d.ts.map +1 -0
  9. package/dist/user-tool-parse/index.js +12 -0
  10. package/dist/user-tool-parse/index.js.map +1 -0
  11. package/dist/user-tool-parse/inputs.d.ts +13 -0
  12. package/dist/user-tool-parse/inputs.d.ts.map +1 -0
  13. package/dist/user-tool-parse/inputs.js +565 -0
  14. package/dist/user-tool-parse/inputs.js.map +1 -0
  15. package/dist/user-tool-parse/outputs.d.ts +10 -0
  16. package/dist/user-tool-parse/outputs.d.ts.map +1 -0
  17. package/dist/user-tool-parse/outputs.js +231 -0
  18. package/dist/user-tool-parse/outputs.js.map +1 -0
  19. package/dist/user-tool-parse/parse.d.ts +12 -0
  20. package/dist/user-tool-parse/parse.d.ts.map +1 -0
  21. package/dist/user-tool-parse/parse.js +98 -0
  22. package/dist/user-tool-parse/parse.js.map +1 -0
  23. package/dist/user-tool-source/index.d.ts +3 -0
  24. package/dist/user-tool-source/index.d.ts.map +1 -0
  25. package/dist/user-tool-source/index.js +3 -0
  26. package/dist/user-tool-source/index.js.map +1 -0
  27. package/dist/user-tool-source/schema.generated.d.ts +7298 -0
  28. package/dist/user-tool-source/schema.generated.d.ts.map +1 -0
  29. package/dist/user-tool-source/schema.generated.js +8851 -0
  30. package/dist/user-tool-source/schema.generated.js.map +1 -0
  31. package/dist/user-tool-source/semantic.d.ts +14 -0
  32. package/dist/user-tool-source/semantic.d.ts.map +1 -0
  33. package/dist/user-tool-source/semantic.js +137 -0
  34. package/dist/user-tool-source/semantic.js.map +1 -0
  35. package/dist/user-tool-source/validate.d.ts +37 -0
  36. package/dist/user-tool-source/validate.d.ts.map +1 -0
  37. package/dist/user-tool-source/validate.js +54 -0
  38. package/dist/user-tool-source/validate.js.map +1 -0
  39. package/dist/workflow/draft-checks.d.ts +205 -0
  40. package/dist/workflow/draft-checks.d.ts.map +1 -0
  41. package/dist/workflow/draft-checks.js +1151 -0
  42. package/dist/workflow/draft-checks.js.map +1 -0
  43. package/dist/workflow/index.d.ts +3 -1
  44. package/dist/workflow/index.d.ts.map +1 -1
  45. package/dist/workflow/index.js +3 -1
  46. package/dist/workflow/index.js.map +1 -1
  47. package/dist/workflow/normalized/format2.d.ts +1 -0
  48. package/dist/workflow/normalized/format2.d.ts.map +1 -1
  49. package/dist/workflow/normalized/format2.js +15 -2
  50. package/dist/workflow/normalized/format2.js.map +1 -1
  51. package/dist/workflow/normalized/native.d.ts +1 -1
  52. package/dist/workflow/normalized/toNative.js +29 -4
  53. package/dist/workflow/normalized/toNative.js.map +1 -1
  54. package/dist/workflow/promote-draft.d.ts +53 -0
  55. package/dist/workflow/promote-draft.d.ts.map +1 -0
  56. package/dist/workflow/promote-draft.js +133 -0
  57. package/dist/workflow/promote-draft.js.map +1 -0
  58. package/dist/workflow/raw/gxformat2-draft.d.ts +688 -0
  59. package/dist/workflow/raw/gxformat2-draft.d.ts.map +1 -0
  60. package/dist/workflow/raw/gxformat2-draft.effect.d.ts +4607 -0
  61. package/dist/workflow/raw/gxformat2-draft.effect.d.ts.map +1 -0
  62. package/dist/workflow/raw/gxformat2-draft.effect.js +778 -0
  63. package/dist/workflow/raw/gxformat2-draft.effect.js.map +1 -0
  64. package/dist/workflow/raw/gxformat2-draft.js +20 -0
  65. package/dist/workflow/raw/gxformat2-draft.js.map +1 -0
  66. package/dist/workflow/raw/gxformat2.d.ts +237 -13
  67. package/dist/workflow/raw/gxformat2.d.ts.map +1 -1
  68. package/dist/workflow/raw/gxformat2.effect.d.ts +1375 -177
  69. package/dist/workflow/raw/gxformat2.effect.d.ts.map +1 -1
  70. package/dist/workflow/raw/gxformat2.effect.js +355 -108
  71. package/dist/workflow/raw/gxformat2.effect.js.map +1 -1
  72. package/dist/workflow/raw/gxformat2.js +18 -1
  73. package/dist/workflow/raw/gxformat2.js.map +1 -1
  74. package/dist/workflow/raw/index.d.ts +2 -0
  75. package/dist/workflow/raw/index.d.ts.map +1 -1
  76. package/dist/workflow/raw/index.js +1 -0
  77. package/dist/workflow/raw/index.js.map +1 -1
  78. package/dist/workflow/raw/native.d.ts +51 -2
  79. package/dist/workflow/raw/native.d.ts.map +1 -1
  80. package/dist/workflow/raw/native.effect.d.ts +82 -30
  81. package/dist/workflow/raw/native.effect.d.ts.map +1 -1
  82. package/dist/workflow/raw/native.effect.js +67 -18
  83. package/dist/workflow/raw/native.effect.js.map +1 -1
  84. package/dist/workflow/raw/native.js.map +1 -1
  85. package/dist/workflow/report-models.d.ts +58 -0
  86. package/dist/workflow/report-models.d.ts.map +1 -1
  87. package/dist/workflow/report-models.js +81 -0
  88. package/dist/workflow/report-models.js.map +1 -1
  89. package/dist/workflow/semantic-validators.d.ts +18 -0
  90. package/dist/workflow/semantic-validators.d.ts.map +1 -0
  91. package/dist/workflow/semantic-validators.js +137 -0
  92. package/dist/workflow/semantic-validators.js.map +1 -0
  93. package/dist/workflow/validators.d.ts.map +1 -1
  94. package/dist/workflow/validators.js +7 -2
  95. package/dist/workflow/validators.js.map +1 -1
  96. package/package.json +1 -1
@@ -15,12 +15,15 @@ string: Unicode character sequence
15
15
  export declare const PrimitiveTypeSchema: Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string"]>;
16
16
  export type PrimitiveType = typeof PrimitiveTypeSchema.Type;
17
17
  /**
18
- * Extends primitive types with the native Galaxy concepts such datasets and collections.
19
- integer: an alias for int type - matches syntax used by Galaxy tools
20
- text: an alias for string type - matches syntax used by Galaxy tools
21
- File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future
22
- data: a Galaxy dataset
23
- collection: a Galaxy dataset collection
18
+ * Extends primitive types with the native Galaxy concepts such as datasets and collections.
19
+ Normalized gxformat2 workflow input declaration spellings are ``data``, ``collection``, ``string``, ``int``, ``float``, and ``boolean``. Other spellings are accepted as compatibility aliases on import but normalized gxformat2 output emits the normalized spellings.
20
+ data: one Galaxy dataset input. Native Galaxy ``data_input`` converts to this spelling.
21
+ File: accepted alias for ``data``, but normalized gxformat2 output emits ``data``. Note: workflow **test job** YAML uses ``type: File`` to mean 'stage this file as test input data', which is a separate concept from workflow input declaration.
22
+ collection: one Galaxy dataset collection input. Native Galaxy ``data_collection_input`` converts to this spelling.
23
+ string: normalized gxformat2 spelling for native Galaxy text workflow parameters.
24
+ text: accepted alias for ``string`` because native Galaxy parameter state and Galaxy tool XML terminology use ``text``.
25
+ int: normalized gxformat2 spelling for native Galaxy integer workflow parameters.
26
+ integer: accepted alias for ``int`` because native Galaxy parameter state and Galaxy tool XML terminology use ``integer``.
24
27
  */
25
28
  export declare const GalaxyTypeSchema: Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>;
26
29
  export type GalaxyType = typeof GalaxyTypeSchema.Type;
@@ -40,13 +43,6 @@ export declare const DocumentedSchema: Schema.Struct<{
40
43
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
41
44
  }>;
42
45
  export type Documented = typeof DocumentedSchema.Type;
43
- export declare const RecordSchemaSchema: Schema.Struct<{
44
- /** Defines the fields of the record. */
45
- fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.suspend<any, any, never>>]>>;
46
- /** Must be `record` */
47
- type: Schema.Literal<["record"]>;
48
- }>;
49
- export type RecordSchema = typeof RecordSchemaSchema.Type;
50
46
  /**
51
47
  * Define an enumerated type.
52
48
  */
@@ -57,6 +53,13 @@ export declare const EnumSchemaSchema: Schema.Struct<{
57
53
  type: Schema.Literal<["enum"]>;
58
54
  }>;
59
55
  export type EnumSchema = typeof EnumSchemaSchema.Type;
56
+ export declare const RecordSchemaSchema: Schema.Struct<{
57
+ /** Defines the fields of the record. */
58
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.suspend<any, any, never>>]>>;
59
+ /** Must be `record` */
60
+ type: Schema.Literal<["record"]>;
61
+ }>;
62
+ export type RecordSchema = typeof RecordSchemaSchema.Type;
60
63
  export declare const ArraySchemaSchema: Schema.Struct<{
61
64
  /** Defines the type of the array elements. */
62
65
  items: Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string"]>, Schema.Struct<{
@@ -223,30 +226,302 @@ export declare const HasStepPositionSchema: Schema.Struct<{
223
226
  }>]>>;
224
227
  }>;
225
228
  export type HasStepPosition = typeof HasStepPositionSchema.Type;
226
- export declare const WorkflowInputParameterSchema: Schema.Struct<{
229
+ export declare const BaseInputParameterSchema: Schema.Struct<{
227
230
  /** The unique identifier for this object. */
228
231
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
229
232
  /** A short, human-readable label of this object. */
230
233
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
231
234
  /** A documentation string for this object, or an array of strings which should be concatenated. */
232
235
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
233
- /** Specify valid types of data that may be assigned to this parameter. */
234
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
235
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
236
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
237
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
238
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
239
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
240
+ top: typeof Schema.Number;
241
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
242
+ left: typeof Schema.Number;
243
+ }>]>>;
244
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
245
+ }>;
246
+ export type BaseInputParameter = typeof BaseInputParameterSchema.Type;
247
+ export declare const MinMaxSchema: Schema.Struct<{
248
+ /** Minimum allowed value (inclusive). */
249
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
250
+ /** Maximum allowed value (inclusive). */
251
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
252
+ }>;
253
+ export type MinMax = typeof MinMaxSchema.Type;
254
+ /**
255
+ * A float input parameter for a Galaxy workflow.
256
+ */
257
+ export declare const WorkflowFloatParameterSchema: Schema.Struct<{
258
+ /** The unique identifier for this object. */
259
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
260
+ /** A short, human-readable label of this object. */
261
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
262
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
263
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
264
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
265
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
266
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
267
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
268
+ top: typeof Schema.Number;
269
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
270
+ left: typeof Schema.Number;
271
+ }>]>>;
272
+ /** Must be ``float``. */
273
+ type: Schema.Literal<["float"]>;
274
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
275
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
276
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
277
+ }>;
278
+ export type WorkflowFloatParameter = typeof WorkflowFloatParameterSchema.Type;
279
+ /**
280
+ * A boolean input parameter for a Galaxy workflow.
281
+ */
282
+ export declare const WorkflowBooleanParameterSchema: Schema.Struct<{
283
+ /** The unique identifier for this object. */
284
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
285
+ /** A short, human-readable label of this object. */
286
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
287
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
288
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
289
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
290
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
291
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
292
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
293
+ top: typeof Schema.Number;
294
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
295
+ left: typeof Schema.Number;
296
+ }>]>>;
297
+ /** Must be ``boolean``. */
298
+ type: Schema.Literal<["boolean"]>;
236
299
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
237
- /** Specify datatype extension for valid input datasets. */
300
+ }>;
301
+ export type WorkflowBooleanParameter = typeof WorkflowBooleanParameterSchema.Type;
302
+ /**
303
+ * Describes one field of a `record` collection input.
304
+ Used in `fields` on a `collection_type` containing `record` (e.g.
305
+ `record`, `list:record`, `sample_sheet:record`). Mirrors a subset of
306
+ the CWL `InputRecordSchema` shape that Galaxy persists on
307
+ `DatasetCollection.fields`.
308
+ */
309
+ export declare const RecordFieldDefinitionSchema: Schema.Struct<{
310
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
311
+ name: typeof Schema.String;
312
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
313
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
314
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
315
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
316
+ }>;
317
+ export type RecordFieldDefinition = typeof RecordFieldDefinitionSchema.Type;
318
+ /**
319
+ * Describes one column of a sample-sheet collection input.
320
+ Used in `column_definitions` on a `collection_type: sample_sheet[:<type>]`
321
+ workflow input.
322
+ */
323
+ export declare const SampleSheetColumnDefinitionSchema: Schema.Struct<{
324
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
325
+ name: typeof Schema.String;
326
+ /** Optional human-readable column description. */
327
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
328
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
329
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
330
+ /** If true, rows may omit a value for this column. */
331
+ optional: typeof Schema.Boolean;
332
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
333
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
334
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
335
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
336
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
337
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
338
+ /** Open suggestion list for this column. */
339
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
340
+ }>;
341
+ export type SampleSheetColumnDefinition = typeof SampleSheetColumnDefinitionSchema.Type;
342
+ export declare const BaseDataParameterSchema: Schema.Struct<{
343
+ /** The unique identifier for this object. */
344
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
345
+ /** A short, human-readable label of this object. */
346
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
347
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
348
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
349
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
350
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
351
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
352
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
353
+ top: typeof Schema.Number;
354
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
355
+ left: typeof Schema.Number;
356
+ }>]>>;
357
+ /** Specify datatype extensions for valid input datasets. */
238
358
  format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
359
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
360
+ }>;
361
+ export type BaseDataParameter = typeof BaseDataParameterSchema.Type;
362
+ /**
363
+ * A collection input parameter for a Galaxy workflow - represents a dataset collection.
364
+ */
365
+ export declare const WorkflowCollectionParameterSchema: Schema.Struct<{
366
+ /** The unique identifier for this object. */
367
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
368
+ /** A short, human-readable label of this object. */
369
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
370
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
371
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
372
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
373
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
374
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
375
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
376
+ top: typeof Schema.Number;
377
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
378
+ left: typeof Schema.Number;
379
+ }>]>>;
380
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
381
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
382
+ /** Must be ``collection``. */
383
+ type: Schema.Literal<["collection"]>;
239
384
  /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
240
385
  collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
386
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
387
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
388
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
389
+ name: typeof Schema.String;
390
+ /** Optional human-readable column description. */
391
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
392
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
393
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
394
+ /** If true, rows may omit a value for this column. */
395
+ optional: typeof Schema.Boolean;
396
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
397
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
398
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
399
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
400
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
401
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
402
+ /** Open suggestion list for this column. */
403
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
404
+ }>>]>>;
405
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
406
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
407
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
408
+ name: typeof Schema.String;
409
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
410
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
411
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
412
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
413
+ }>>]>>;
414
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
415
+ }>;
416
+ export type WorkflowCollectionParameter = typeof WorkflowCollectionParameterSchema.Type;
417
+ /**
418
+ * A scalar integer workflow parameter. Normalized gxformat2 output uses
419
+ ``type: int``. ``type: integer`` is accepted for compatibility with native
420
+ Galaxy parameter state and Galaxy tool XML terminology.
421
+ */
422
+ export declare const WorkflowIntegerParameterSchema: Schema.Struct<{
423
+ /** The unique identifier for this object. */
424
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
425
+ /** A short, human-readable label of this object. */
426
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
427
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
428
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
429
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
430
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
431
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
432
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
433
+ top: typeof Schema.Number;
434
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
435
+ left: typeof Schema.Number;
436
+ }>]>>;
437
+ /** Must be ``integer`` or ``int``. */
438
+ type: Schema.Literal<["integer", "int"]>;
439
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
440
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
441
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
442
+ }>;
443
+ export type WorkflowIntegerParameter = typeof WorkflowIntegerParameterSchema.Type;
444
+ /**
445
+ * A data input parameter for a Galaxy workflow. Represents one Galaxy dataset.
446
+ Normalized gxformat2 output uses ``type: data``. ``type: File`` is accepted as
447
+ an alias, but should not be confused with workflow test job syntax where
448
+ ``type: File`` means stage a file as test input data.
449
+ */
450
+ export declare const WorkflowDataParameterSchema: Schema.Struct<{
451
+ /** The unique identifier for this object. */
452
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
453
+ /** A short, human-readable label of this object. */
454
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
455
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
456
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
457
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
458
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
241
459
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
242
460
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
243
461
  top: typeof Schema.Number;
244
462
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
245
463
  left: typeof Schema.Number;
246
464
  }>]>>;
465
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
466
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
467
+ /** Specify valid types of data that may be assigned to this parameter. */
468
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
469
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
470
+ }>;
471
+ export type WorkflowDataParameter = typeof WorkflowDataParameterSchema.Type;
472
+ /**
473
+ * A `{value, label}` option used in `restrictions` or `suggestions` on a
474
+ text workflow parameter. Plain strings are also accepted in those
475
+ arrays as shorthand for `{value: <str>, label: <str>}`.
476
+ */
477
+ export declare const WorkflowTextOptionSchema: Schema.Struct<{
478
+ /** Machine value submitted to the connected tool input. */
479
+ value: typeof Schema.String;
480
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
481
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
482
+ }>;
483
+ export type WorkflowTextOption = typeof WorkflowTextOptionSchema.Type;
484
+ /**
485
+ * A scalar text workflow parameter. Normalized gxformat2 output uses
486
+ ``type: string``. ``type: text`` is accepted for compatibility with native
487
+ Galaxy parameter state and Galaxy tool XML terminology.
488
+ */
489
+ export declare const WorkflowTextParameterSchema: Schema.Struct<{
490
+ /** The unique identifier for this object. */
491
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
492
+ /** A short, human-readable label of this object. */
493
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
494
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
495
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
496
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
247
497
  default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
498
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
499
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
500
+ top: typeof Schema.Number;
501
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
502
+ left: typeof Schema.Number;
503
+ }>]>>;
504
+ /** Must be ``text`` or ``string``. */
505
+ type: Schema.Literal<["text", "string"]>;
506
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
507
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
508
+ /** Machine value submitted to the connected tool input. */
509
+ value: typeof Schema.String;
510
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
511
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
512
+ }>]>>]>>;
513
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
514
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
515
+ /** Machine value submitted to the connected tool input. */
516
+ value: typeof Schema.String;
517
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
518
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
519
+ }>]>>]>>;
520
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
521
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
522
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
248
523
  }>;
249
- export type WorkflowInputParameter = typeof WorkflowInputParameterSchema.Type;
524
+ export type WorkflowTextParameter = typeof WorkflowTextParameterSchema.Type;
250
525
  /**
251
526
  * Describe an output parameter of a workflow. The parameter must be
252
527
  connected to one parameter defined in the workflow that
@@ -273,73 +548,353 @@ directly executed.
273
548
  */
274
549
  export declare const ProcessSchema: Schema.Struct<{
275
550
  /** Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each paramet... */
276
- inputs: Schema.Union<[Schema.Array$<Schema.Struct<{
551
+ inputs: Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
277
552
  /** The unique identifier for this object. */
278
553
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
279
554
  /** A short, human-readable label of this object. */
280
555
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
281
556
  /** A documentation string for this object, or an array of strings which should be concatenated. */
282
557
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
283
- /** Specify valid types of data that may be assigned to this parameter. */
284
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
285
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
558
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
559
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
560
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
561
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
562
+ top: typeof Schema.Number;
563
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
564
+ left: typeof Schema.Number;
565
+ }>]>>;
566
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
286
567
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
287
- /** Specify datatype extension for valid input datasets. */
568
+ /** Specify valid types of data that may be assigned to this parameter. */
569
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
288
570
  format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
571
+ }>, Schema.Struct<{
572
+ /** The unique identifier for this object. */
573
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
574
+ /** A short, human-readable label of this object. */
575
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
576
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
577
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
578
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
579
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
580
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
581
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
582
+ top: typeof Schema.Number;
583
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
584
+ left: typeof Schema.Number;
585
+ }>]>>;
586
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
587
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
588
+ /** Must be ``collection``. */
589
+ type: Schema.Literal<["collection"]>;
289
590
  /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
290
591
  collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
592
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
593
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
594
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
595
+ name: typeof Schema.String;
596
+ /** Optional human-readable column description. */
597
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
598
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
599
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
600
+ /** If true, rows may omit a value for this column. */
601
+ optional: typeof Schema.Boolean;
602
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
603
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
604
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
605
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
606
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
607
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
608
+ /** Open suggestion list for this column. */
609
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
610
+ }>>]>>;
611
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
612
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
613
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
614
+ name: typeof Schema.String;
615
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
616
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
617
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
618
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
619
+ }>>]>>;
620
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
621
+ }>, Schema.Struct<{
622
+ /** The unique identifier for this object. */
623
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
624
+ /** A short, human-readable label of this object. */
625
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
626
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
627
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
628
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
629
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
291
630
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
292
631
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
293
632
  top: typeof Schema.Number;
294
633
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
295
634
  left: typeof Schema.Number;
296
635
  }>]>>;
297
- default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
298
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
636
+ /** Must be ``integer`` or ``int``. */
637
+ type: Schema.Literal<["integer", "int"]>;
638
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
639
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
640
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
641
+ }>, Schema.Struct<{
299
642
  /** The unique identifier for this object. */
300
643
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
301
644
  /** A short, human-readable label of this object. */
302
645
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
303
646
  /** A documentation string for this object, or an array of strings which should be concatenated. */
304
647
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
305
- /** Specify valid types of data that may be assigned to this parameter. */
306
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
307
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
648
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
649
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
650
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
651
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
652
+ top: typeof Schema.Number;
653
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
654
+ left: typeof Schema.Number;
655
+ }>]>>;
656
+ /** Must be ``float``. */
657
+ type: Schema.Literal<["float"]>;
658
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
659
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
308
660
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
309
- /** Specify datatype extension for valid input datasets. */
310
- format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
311
- /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
312
- collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
661
+ }>, Schema.Struct<{
662
+ /** The unique identifier for this object. */
663
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
664
+ /** A short, human-readable label of this object. */
665
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
666
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
667
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
668
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
669
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
313
670
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
314
671
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
315
672
  top: typeof Schema.Number;
316
673
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
317
674
  left: typeof Schema.Number;
318
675
  }>]>>;
676
+ /** Must be ``text`` or ``string``. */
677
+ type: Schema.Literal<["text", "string"]>;
678
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
679
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
680
+ /** Machine value submitted to the connected tool input. */
681
+ value: typeof Schema.String;
682
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
683
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
684
+ }>]>>]>>;
685
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
686
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
687
+ /** Machine value submitted to the connected tool input. */
688
+ value: typeof Schema.String;
689
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
690
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
691
+ }>]>>]>>;
692
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
693
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
694
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
695
+ }>, Schema.Struct<{
696
+ /** The unique identifier for this object. */
697
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
698
+ /** A short, human-readable label of this object. */
699
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
700
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
701
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
702
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
319
703
  default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
320
- }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
321
- /** Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. */
322
- outputs: Schema.Union<[Schema.Array$<Schema.Struct<{
704
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
705
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
706
+ top: typeof Schema.Number;
707
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
708
+ left: typeof Schema.Number;
709
+ }>]>>;
710
+ /** Must be ``boolean``. */
711
+ type: Schema.Literal<["boolean"]>;
712
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
713
+ }>]>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
323
714
  /** The unique identifier for this object. */
324
715
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
325
716
  /** A short, human-readable label of this object. */
326
717
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
327
718
  /** A documentation string for this object, or an array of strings which should be concatenated. */
328
719
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
329
- /** Specifies workflow parameter that supply the value of to the output parameter. */
330
- outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
720
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
721
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
722
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
723
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
724
+ top: typeof Schema.Number;
725
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
726
+ left: typeof Schema.Number;
727
+ }>]>>;
728
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
729
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
331
730
  /** Specify valid types of data that may be assigned to this parameter. */
332
- type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
333
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
731
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
732
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
733
+ }>, Schema.Struct<{
334
734
  /** The unique identifier for this object. */
335
735
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
336
736
  /** A short, human-readable label of this object. */
337
737
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
338
738
  /** A documentation string for this object, or an array of strings which should be concatenated. */
339
739
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
340
- /** Specifies workflow parameter that supply the value of to the output parameter. */
341
- outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
342
- /** Specify valid types of data that may be assigned to this parameter. */
740
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
741
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
742
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
743
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
744
+ top: typeof Schema.Number;
745
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
746
+ left: typeof Schema.Number;
747
+ }>]>>;
748
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
749
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
750
+ /** Must be ``collection``. */
751
+ type: Schema.Literal<["collection"]>;
752
+ /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
753
+ collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
754
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
755
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
756
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
757
+ name: typeof Schema.String;
758
+ /** Optional human-readable column description. */
759
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
760
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
761
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
762
+ /** If true, rows may omit a value for this column. */
763
+ optional: typeof Schema.Boolean;
764
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
765
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
766
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
767
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
768
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
769
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
770
+ /** Open suggestion list for this column. */
771
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
772
+ }>>]>>;
773
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
774
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
775
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
776
+ name: typeof Schema.String;
777
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
778
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
779
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
780
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
781
+ }>>]>>;
782
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
783
+ }>, Schema.Struct<{
784
+ /** The unique identifier for this object. */
785
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
786
+ /** A short, human-readable label of this object. */
787
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
788
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
789
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
790
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
791
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
792
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
793
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
794
+ top: typeof Schema.Number;
795
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
796
+ left: typeof Schema.Number;
797
+ }>]>>;
798
+ /** Must be ``integer`` or ``int``. */
799
+ type: Schema.Literal<["integer", "int"]>;
800
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
801
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
802
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
803
+ }>, Schema.Struct<{
804
+ /** The unique identifier for this object. */
805
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
806
+ /** A short, human-readable label of this object. */
807
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
808
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
809
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
810
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
811
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
812
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
813
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
814
+ top: typeof Schema.Number;
815
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
816
+ left: typeof Schema.Number;
817
+ }>]>>;
818
+ /** Must be ``float``. */
819
+ type: Schema.Literal<["float"]>;
820
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
821
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
822
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
823
+ }>, Schema.Struct<{
824
+ /** The unique identifier for this object. */
825
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
826
+ /** A short, human-readable label of this object. */
827
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
828
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
829
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
830
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
831
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
832
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
833
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
834
+ top: typeof Schema.Number;
835
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
836
+ left: typeof Schema.Number;
837
+ }>]>>;
838
+ /** Must be ``text`` or ``string``. */
839
+ type: Schema.Literal<["text", "string"]>;
840
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
841
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
842
+ /** Machine value submitted to the connected tool input. */
843
+ value: typeof Schema.String;
844
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
845
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
846
+ }>]>>]>>;
847
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
848
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
849
+ /** Machine value submitted to the connected tool input. */
850
+ value: typeof Schema.String;
851
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
852
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
853
+ }>]>>]>>;
854
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
855
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
856
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
857
+ }>, Schema.Struct<{
858
+ /** The unique identifier for this object. */
859
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
860
+ /** A short, human-readable label of this object. */
861
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
862
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
863
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
864
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
865
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
866
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
867
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
868
+ top: typeof Schema.Number;
869
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
870
+ left: typeof Schema.Number;
871
+ }>]>>;
872
+ /** Must be ``boolean``. */
873
+ type: Schema.Literal<["boolean"]>;
874
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
875
+ }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
876
+ /** Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. */
877
+ outputs: Schema.Union<[Schema.Array$<Schema.Struct<{
878
+ /** The unique identifier for this object. */
879
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
880
+ /** A short, human-readable label of this object. */
881
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
882
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
883
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
884
+ /** Specifies workflow parameter that supply the value of to the output parameter. */
885
+ outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
886
+ /** Specify valid types of data that may be assigned to this parameter. */
887
+ type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
888
+ }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
889
+ /** The unique identifier for this object. */
890
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
891
+ /** A short, human-readable label of this object. */
892
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
893
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
894
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
895
+ /** Specifies workflow parameter that supply the value of to the output parameter. */
896
+ outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
897
+ /** Specify valid types of data that may be assigned to this parameter. */
343
898
  type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
344
899
  }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
345
900
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
@@ -387,44 +942,117 @@ export declare const ReferencesToolSchema: Schema.Struct<{
387
942
  }>;
388
943
  export type ReferencesTool = typeof ReferencesToolSchema.Type;
389
944
  /**
390
- * Definition of an invocation report for this workflow. Currently the only
391
- field is 'markdown'.
945
+ * An input parameter to a Galaxy workflow. This is the catch-all type used
946
+ by the Schema Salad codegen. The pydantic layer uses a discriminated union
947
+ of the specific parameter types instead.
392
948
  */
393
- export declare const ReportSchema: Schema.Struct<{
394
- /** Galaxy flavored Markdown to define an invocation report. */
395
- markdown: typeof Schema.String;
949
+ export declare const WorkflowInputParameterSchema: Schema.Struct<{
950
+ /** The unique identifier for this object. */
951
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
952
+ /** A short, human-readable label of this object. */
953
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
954
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
955
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
956
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
957
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
958
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
959
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
960
+ top: typeof Schema.Number;
961
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
962
+ left: typeof Schema.Number;
963
+ }>]>>;
964
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
965
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
966
+ /** Specify valid types of data that may be assigned to this parameter. */
967
+ type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
968
+ /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
969
+ collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
970
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet`. */
971
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
972
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
973
+ name: typeof Schema.String;
974
+ /** Optional human-readable column description. */
975
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
976
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
977
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
978
+ /** If true, rows may omit a value for this column. */
979
+ optional: typeof Schema.Boolean;
980
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
981
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
982
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
983
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
984
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
985
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
986
+ /** Open suggestion list for this column. */
987
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
988
+ }>>]>>;
989
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record`. */
990
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
991
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
992
+ name: typeof Schema.String;
993
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
994
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
995
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
996
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
997
+ }>>]>>;
998
+ /** Closed set of permitted values for text-typed inputs. See `WorkflowTextParameter.restrictions`. */
999
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1000
+ /** Machine value submitted to the connected tool input. */
1001
+ value: typeof Schema.String;
1002
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1003
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1004
+ }>]>>]>>;
1005
+ /** Open suggestion list for text-typed inputs. */
1006
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1007
+ /** Machine value submitted to the connected tool input. */
1008
+ value: typeof Schema.String;
1009
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1010
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1011
+ }>]>>]>>;
1012
+ /** For text-typed inputs - derive runtime choices from connected tool/subworkflow select inputs. */
1013
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1014
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1015
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1016
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
396
1017
  }>;
397
- export type Report = typeof ReportSchema.Type;
1018
+ export type WorkflowInputParameter = typeof WorkflowInputParameterSchema.Type;
398
1019
  /**
399
- * Base fields shared by all comment types.
1020
+ * Associate an output parameter of the underlying process with a workflow
1021
+ parameter. The workflow parameter (given in the `id` field) be may be used
1022
+ as a `source` to connect with input parameters of other workflow steps, or
1023
+ with an output parameter of the process.
1024
+
1025
+ A unique identifier for this workflow output parameter. This is
1026
+ the identifier to use in the `source` field of `WorkflowStepInput`
1027
+ to connect the output value to downstream parameters.
400
1028
  */
401
- export declare const BaseCommentSchema: Schema.Struct<{
402
- /** Position of the comment on the editor canvas as ``[x, y]`` coordinates. */
403
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
404
- /** Size of the comment as ``[width, height]``. */
405
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
406
- /** Display color of the comment (e.g. ``"none"``, ``"blue"``). */
407
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
408
- /** Optional label for referencing this comment from frame ``contains_comments`` fields or for use as a map key when comments are represented as a mapping. */
409
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1029
+ export declare const WorkflowStepOutputSchema: Schema.Struct<{
1030
+ add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1031
+ change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1032
+ delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1033
+ hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1034
+ remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1035
+ rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1036
+ set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
1037
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
410
1038
  }>;
411
- export type BaseComment = typeof BaseCommentSchema.Type;
1039
+ export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
1040
+ export declare const SinkSchema: Schema.Struct<{
1041
+ /** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
1042
+ source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1043
+ }>;
1044
+ export type Sink = typeof SinkSchema.Type;
412
1045
  /**
413
- * A freehand drawn line on the editor canvas.
1046
+ * TODO:
414
1047
  */
415
- export declare const FreehandCommentSchema: Schema.Struct<{
416
- /** Comment type (``freehand``). */
417
- type: Schema.Literal<["freehand"]>;
418
- /** Line thickness. */
419
- thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
420
- /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
421
- line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
422
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
423
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
424
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1048
+ export declare const WorkflowStepInputSchema: Schema.Struct<{
1049
+ /** The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`. The default must be applied prior to scattering or evaluating `va... */
1050
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
425
1051
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1052
+ source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1053
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
426
1054
  }>;
427
- export type FreehandComment = typeof FreehandCommentSchema.Type;
1055
+ export type WorkflowStepInput = typeof WorkflowStepInputSchema.Type;
428
1056
  /**
429
1057
  * Base fields shared by all creator types, corresponding to schema.org
430
1058
  Thing properties common to both Person and Organization.
@@ -450,6 +1078,61 @@ export declare const BaseCreatorSchema: Schema.Struct<{
450
1078
  faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
451
1079
  }>;
452
1080
  export type BaseCreator = typeof BaseCreatorSchema.Type;
1081
+ /**
1082
+ * An organization that created or contributed to the workflow.
1083
+ Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
1084
+ */
1085
+ export declare const CreatorOrganizationSchema: Schema.Struct<{
1086
+ /** Creator type discriminator (``Organization``). */
1087
+ class: Schema.Literal<["Organization"]>;
1088
+ name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1089
+ identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1090
+ url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1091
+ email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1092
+ image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1093
+ address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1094
+ alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1095
+ telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1096
+ faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1097
+ }>;
1098
+ export type CreatorOrganization = typeof CreatorOrganizationSchema.Type;
1099
+ /**
1100
+ * Definition of an invocation report for this workflow. Currently the only
1101
+ field is 'markdown'.
1102
+ */
1103
+ export declare const ReportSchema: Schema.Struct<{
1104
+ /** Galaxy flavored Markdown to define an invocation report. */
1105
+ markdown: typeof Schema.String;
1106
+ }>;
1107
+ export type Report = typeof ReportSchema.Type;
1108
+ /**
1109
+ * Base fields shared by all comment types.
1110
+ */
1111
+ export declare const BaseCommentSchema: Schema.Struct<{
1112
+ /** Position of the comment on the editor canvas as ``[x, y]`` coordinates. */
1113
+ position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1114
+ /** Size of the comment as ``[width, height]``. */
1115
+ size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1116
+ /** Display color of the comment (e.g. ``"none"``, ``"blue"``). */
1117
+ color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1118
+ /** Optional label for referencing this comment from frame ``contains_comments`` fields or for use as a map key when comments are represented as a mapping. */
1119
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1120
+ }>;
1121
+ export type BaseComment = typeof BaseCommentSchema.Type;
1122
+ /**
1123
+ * A Markdown-rendered annotation in the workflow editor.
1124
+ */
1125
+ export declare const MarkdownCommentSchema: Schema.Struct<{
1126
+ /** Comment type (``markdown``). */
1127
+ type: Schema.Literal<["markdown"]>;
1128
+ /** Markdown content. */
1129
+ text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1130
+ position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1131
+ size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1132
+ color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1133
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1134
+ }>;
1135
+ export type MarkdownComment = typeof MarkdownCommentSchema.Type;
453
1136
  /**
454
1137
  * A person who created or contributed to the workflow.
455
1138
  Corresponds to a `schema.org Person <https://schema.org/Person>`_.
@@ -478,26 +1161,6 @@ export declare const CreatorPersonSchema: Schema.Struct<{
478
1161
  faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
479
1162
  }>;
480
1163
  export type CreatorPerson = typeof CreatorPersonSchema.Type;
481
- /**
482
- * A plain text annotation in the workflow editor.
483
- */
484
- export declare const TextCommentSchema: Schema.Struct<{
485
- /** Comment type (``text``). */
486
- type: Schema.Literal<["text"]>;
487
- /** The text content. */
488
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
489
- /** Whether the text is displayed in bold. */
490
- bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
491
- /** Whether the text is displayed in italic. */
492
- italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
493
- /** Font size of the text. */
494
- text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
495
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
496
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
497
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
498
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
499
- }>;
500
- export type TextComment = typeof TextCommentSchema.Type;
501
1164
  /**
502
1165
  * A rectangular grouping box that visually contains steps and other comments.
503
1166
  */
@@ -517,37 +1180,41 @@ export declare const FrameCommentSchema: Schema.Struct<{
517
1180
  }>;
518
1181
  export type FrameComment = typeof FrameCommentSchema.Type;
519
1182
  /**
520
- * A Markdown-rendered annotation in the workflow editor.
1183
+ * A freehand drawn line on the editor canvas.
521
1184
  */
522
- export declare const MarkdownCommentSchema: Schema.Struct<{
523
- /** Comment type (``markdown``). */
524
- type: Schema.Literal<["markdown"]>;
525
- /** Markdown content. */
526
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1185
+ export declare const FreehandCommentSchema: Schema.Struct<{
1186
+ /** Comment type (``freehand``). */
1187
+ type: Schema.Literal<["freehand"]>;
1188
+ /** Line thickness. */
1189
+ thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
1190
+ /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
1191
+ line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
527
1192
  position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
528
1193
  size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
529
1194
  color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
530
1195
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
531
1196
  }>;
532
- export type MarkdownComment = typeof MarkdownCommentSchema.Type;
1197
+ export type FreehandComment = typeof FreehandCommentSchema.Type;
533
1198
  /**
534
- * An organization that created or contributed to the workflow.
535
- Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
1199
+ * A plain text annotation in the workflow editor.
536
1200
  */
537
- export declare const CreatorOrganizationSchema: Schema.Struct<{
538
- /** Creator type discriminator (``Organization``). */
539
- class: Schema.Literal<["Organization"]>;
540
- name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
541
- identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
542
- url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
543
- email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
544
- image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
545
- address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
546
- alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
547
- telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
548
- faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1201
+ export declare const TextCommentSchema: Schema.Struct<{
1202
+ /** Comment type (``text``). */
1203
+ type: Schema.Literal<["text"]>;
1204
+ /** The text content. */
1205
+ text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1206
+ /** Whether the text is displayed in bold. */
1207
+ bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1208
+ /** Whether the text is displayed in italic. */
1209
+ italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1210
+ /** Font size of the text. */
1211
+ text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
1212
+ position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1213
+ size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
1214
+ color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1215
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
549
1216
  }>;
550
- export type CreatorOrganization = typeof CreatorOrganizationSchema.Type;
1217
+ export type TextComment = typeof TextCommentSchema.Type;
551
1218
  /**
552
1219
  * A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable
553
1220
  on a Galaxy server that includes the contained tool definitions.
@@ -718,50 +1385,330 @@ export declare const GalaxyWorkflowSchema: Schema.Struct<{
718
1385
  /** If listed should correspond to the release of the workflow in its source reposiory. */
719
1386
  release: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
720
1387
  uuid: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
721
- inputs: Schema.Union<[Schema.Array$<Schema.Struct<{
1388
+ inputs: Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
1389
+ /** The unique identifier for this object. */
1390
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1391
+ /** A short, human-readable label of this object. */
1392
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1393
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1394
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1395
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1396
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1397
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1398
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1399
+ top: typeof Schema.Number;
1400
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1401
+ left: typeof Schema.Number;
1402
+ }>]>>;
1403
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1404
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1405
+ /** Specify valid types of data that may be assigned to this parameter. */
1406
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
1407
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1408
+ }>, Schema.Struct<{
1409
+ /** The unique identifier for this object. */
1410
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1411
+ /** A short, human-readable label of this object. */
1412
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1413
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1414
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1415
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1416
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1417
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1418
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1419
+ top: typeof Schema.Number;
1420
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1421
+ left: typeof Schema.Number;
1422
+ }>]>>;
1423
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1424
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1425
+ /** Must be ``collection``. */
1426
+ type: Schema.Literal<["collection"]>;
1427
+ /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
1428
+ collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1429
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
1430
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
1431
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
1432
+ name: typeof Schema.String;
1433
+ /** Optional human-readable column description. */
1434
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1435
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
1436
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
1437
+ /** If true, rows may omit a value for this column. */
1438
+ optional: typeof Schema.Boolean;
1439
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
1440
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
1441
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
1442
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
1443
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
1444
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
1445
+ /** Open suggestion list for this column. */
1446
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
1447
+ }>>]>>;
1448
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
1449
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
1450
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
1451
+ name: typeof Schema.String;
1452
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
1453
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
1454
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
1455
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1456
+ }>>]>>;
1457
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1458
+ }>, Schema.Struct<{
1459
+ /** The unique identifier for this object. */
1460
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1461
+ /** A short, human-readable label of this object. */
1462
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1463
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1464
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1465
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1466
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1467
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1468
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1469
+ top: typeof Schema.Number;
1470
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1471
+ left: typeof Schema.Number;
1472
+ }>]>>;
1473
+ /** Must be ``integer`` or ``int``. */
1474
+ type: Schema.Literal<["integer", "int"]>;
1475
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1476
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1477
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1478
+ }>, Schema.Struct<{
1479
+ /** The unique identifier for this object. */
1480
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1481
+ /** A short, human-readable label of this object. */
1482
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1483
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1484
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1485
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1486
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1487
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1488
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1489
+ top: typeof Schema.Number;
1490
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1491
+ left: typeof Schema.Number;
1492
+ }>]>>;
1493
+ /** Must be ``float``. */
1494
+ type: Schema.Literal<["float"]>;
1495
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1496
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1497
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1498
+ }>, Schema.Struct<{
1499
+ /** The unique identifier for this object. */
1500
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1501
+ /** A short, human-readable label of this object. */
1502
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1503
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1504
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1505
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1506
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1507
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1508
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1509
+ top: typeof Schema.Number;
1510
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1511
+ left: typeof Schema.Number;
1512
+ }>]>>;
1513
+ /** Must be ``text`` or ``string``. */
1514
+ type: Schema.Literal<["text", "string"]>;
1515
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
1516
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1517
+ /** Machine value submitted to the connected tool input. */
1518
+ value: typeof Schema.String;
1519
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1520
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1521
+ }>]>>]>>;
1522
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
1523
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1524
+ /** Machine value submitted to the connected tool input. */
1525
+ value: typeof Schema.String;
1526
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1527
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1528
+ }>]>>]>>;
1529
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
1530
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1531
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1532
+ }>, Schema.Struct<{
1533
+ /** The unique identifier for this object. */
1534
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1535
+ /** A short, human-readable label of this object. */
1536
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1537
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1538
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1539
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1540
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1541
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1542
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1543
+ top: typeof Schema.Number;
1544
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1545
+ left: typeof Schema.Number;
1546
+ }>]>>;
1547
+ /** Must be ``boolean``. */
1548
+ type: Schema.Literal<["boolean"]>;
1549
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1550
+ }>]>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
1551
+ /** The unique identifier for this object. */
1552
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1553
+ /** A short, human-readable label of this object. */
1554
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1555
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1556
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1557
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1558
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1559
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1560
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1561
+ top: typeof Schema.Number;
1562
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1563
+ left: typeof Schema.Number;
1564
+ }>]>>;
1565
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1566
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1567
+ /** Specify valid types of data that may be assigned to this parameter. */
1568
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
1569
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1570
+ }>, Schema.Struct<{
722
1571
  /** The unique identifier for this object. */
723
1572
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
724
1573
  /** A short, human-readable label of this object. */
725
1574
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
726
1575
  /** A documentation string for this object, or an array of strings which should be concatenated. */
727
1576
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
728
- /** Specify valid types of data that may be assigned to this parameter. */
729
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
730
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
1577
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1578
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1579
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1580
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1581
+ top: typeof Schema.Number;
1582
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1583
+ left: typeof Schema.Number;
1584
+ }>]>>;
1585
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
731
1586
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
732
- /** Specify datatype extension for valid input datasets. */
733
- format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1587
+ /** Must be ``collection``. */
1588
+ type: Schema.Literal<["collection"]>;
734
1589
  /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
735
1590
  collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1591
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
1592
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
1593
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
1594
+ name: typeof Schema.String;
1595
+ /** Optional human-readable column description. */
1596
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1597
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
1598
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
1599
+ /** If true, rows may omit a value for this column. */
1600
+ optional: typeof Schema.Boolean;
1601
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
1602
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
1603
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
1604
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
1605
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
1606
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
1607
+ /** Open suggestion list for this column. */
1608
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
1609
+ }>>]>>;
1610
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
1611
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
1612
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
1613
+ name: typeof Schema.String;
1614
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
1615
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
1616
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
1617
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1618
+ }>>]>>;
1619
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1620
+ }>, Schema.Struct<{
1621
+ /** The unique identifier for this object. */
1622
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1623
+ /** A short, human-readable label of this object. */
1624
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1625
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1626
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1627
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1628
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
736
1629
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
737
1630
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
738
1631
  top: typeof Schema.Number;
739
1632
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
740
1633
  left: typeof Schema.Number;
741
1634
  }>]>>;
742
- default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
743
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
1635
+ /** Must be ``integer`` or ``int``. */
1636
+ type: Schema.Literal<["integer", "int"]>;
1637
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1638
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1639
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1640
+ }>, Schema.Struct<{
744
1641
  /** The unique identifier for this object. */
745
1642
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
746
1643
  /** A short, human-readable label of this object. */
747
1644
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
748
1645
  /** A documentation string for this object, or an array of strings which should be concatenated. */
749
1646
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
750
- /** Specify valid types of data that may be assigned to this parameter. */
751
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
752
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
1647
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1648
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1649
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1650
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1651
+ top: typeof Schema.Number;
1652
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1653
+ left: typeof Schema.Number;
1654
+ }>]>>;
1655
+ /** Must be ``float``. */
1656
+ type: Schema.Literal<["float"]>;
1657
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
1658
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
753
1659
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
754
- /** Specify datatype extension for valid input datasets. */
755
- format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
756
- /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
757
- collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1660
+ }>, Schema.Struct<{
1661
+ /** The unique identifier for this object. */
1662
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1663
+ /** A short, human-readable label of this object. */
1664
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1665
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1666
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1667
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1668
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
758
1669
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
759
1670
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
760
1671
  top: typeof Schema.Number;
761
1672
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
762
1673
  left: typeof Schema.Number;
763
1674
  }>]>>;
1675
+ /** Must be ``text`` or ``string``. */
1676
+ type: Schema.Literal<["text", "string"]>;
1677
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
1678
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1679
+ /** Machine value submitted to the connected tool input. */
1680
+ value: typeof Schema.String;
1681
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1682
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1683
+ }>]>>]>>;
1684
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
1685
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
1686
+ /** Machine value submitted to the connected tool input. */
1687
+ value: typeof Schema.String;
1688
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
1689
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1690
+ }>]>>]>>;
1691
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
1692
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
1693
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1694
+ }>, Schema.Struct<{
1695
+ /** The unique identifier for this object. */
1696
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1697
+ /** A short, human-readable label of this object. */
1698
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1699
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1700
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1701
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
764
1702
  default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1703
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1704
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1705
+ top: typeof Schema.Number;
1706
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1707
+ left: typeof Schema.Number;
1708
+ }>]>>;
1709
+ /** Must be ``boolean``. */
1710
+ type: Schema.Literal<["boolean"]>;
1711
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
765
1712
  }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
766
1713
  outputs: Schema.Union<[Schema.Array$<Schema.Struct<{
767
1714
  /** The unique identifier for this object. */
@@ -788,43 +1735,6 @@ export declare const GalaxyWorkflowSchema: Schema.Struct<{
788
1735
  }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
789
1736
  }>;
790
1737
  export type GalaxyWorkflow = typeof GalaxyWorkflowSchema.Type;
791
- /**
792
- * Associate an output parameter of the underlying process with a workflow
793
- parameter. The workflow parameter (given in the `id` field) be may be used
794
- as a `source` to connect with input parameters of other workflow steps, or
795
- with an output parameter of the process.
796
-
797
- A unique identifier for this workflow output parameter. This is
798
- the identifier to use in the `source` field of `WorkflowStepInput`
799
- to connect the output value to downstream parameters.
800
- */
801
- export declare const WorkflowStepOutputSchema: Schema.Struct<{
802
- add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
803
- change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
804
- delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
805
- hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
806
- remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
807
- rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
808
- set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
809
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
810
- }>;
811
- export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
812
- export declare const SinkSchema: Schema.Struct<{
813
- /** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
814
- source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
815
- }>;
816
- export type Sink = typeof SinkSchema.Type;
817
- /**
818
- * TODO:
819
- */
820
- export declare const WorkflowStepInputSchema: Schema.Struct<{
821
- /** The default value for this parameter to use if either there is no `source` field, or the value produced by the `source` is `null`. The default must be applied prior to scattering or evaluating `va... */
822
- default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
823
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
824
- source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
825
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
826
- }>;
827
- export type WorkflowStepInput = typeof WorkflowStepInputSchema.Type;
828
1738
  /**
829
1739
  * This represents a non-input step a Galaxy Workflow.
830
1740
 
@@ -856,7 +1766,7 @@ export declare const WorkflowStepSchema: Schema.Struct<{
856
1766
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
857
1767
  source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
858
1768
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
859
- }>, typeof Schema.String]>>, typeof Schema.Null]>>;
1769
+ }>, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>, typeof Schema.Null]>>;
860
1770
  /** Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. This can also be called 'outputs' for legacy reasons - but the resulting ... */
861
1771
  out: Schema.optional<Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
862
1772
  add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
@@ -881,6 +1791,8 @@ export declare const WorkflowStepSchema: Schema.Struct<{
881
1791
  state: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
882
1792
  /** Unstructured tool state. */
883
1793
  tool_state: Schema.optional<Schema.Union<[typeof Schema.String, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
1794
+ /** Optional dict of post-job actions keyed by ``{ActionType}{OutputName}`` compound strings. Same shape as the native ``post_job_actions`` field; each value is a record with ``action_type``, ``output... */
1795
+ post_job_actions: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
884
1796
  /** Workflow step module's type (defaults to 'tool'). */
885
1797
  type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["tool", "subworkflow", "pause", "pick_value"]>]>>;
886
1798
  /** Specifies a subworkflow to run. May be an inline workflow definition, a URL string, or an @import reference dict. */
@@ -1040,50 +1952,330 @@ export declare const WorkflowStepSchema: Schema.Struct<{
1040
1952
  /** If listed should correspond to the release of the workflow in its source reposiory. */
1041
1953
  release: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1042
1954
  uuid: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1043
- inputs: Schema.Union<[Schema.Array$<Schema.Struct<{
1955
+ inputs: Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
1044
1956
  /** The unique identifier for this object. */
1045
1957
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1046
1958
  /** A short, human-readable label of this object. */
1047
1959
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1048
1960
  /** A documentation string for this object, or an array of strings which should be concatenated. */
1049
1961
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1050
- /** Specify valid types of data that may be assigned to this parameter. */
1051
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
1052
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
1962
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1963
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1964
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1965
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1966
+ top: typeof Schema.Number;
1967
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1968
+ left: typeof Schema.Number;
1969
+ }>]>>;
1970
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1053
1971
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1054
- /** Specify datatype extension for valid input datasets. */
1972
+ /** Specify valid types of data that may be assigned to this parameter. */
1973
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
1055
1974
  format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1975
+ }>, Schema.Struct<{
1976
+ /** The unique identifier for this object. */
1977
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1978
+ /** A short, human-readable label of this object. */
1979
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1980
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
1981
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1982
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1983
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1984
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1985
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
1986
+ top: typeof Schema.Number;
1987
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1988
+ left: typeof Schema.Number;
1989
+ }>]>>;
1990
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1991
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1992
+ /** Must be ``collection``. */
1993
+ type: Schema.Literal<["collection"]>;
1056
1994
  /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
1057
1995
  collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1996
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
1997
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
1998
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
1999
+ name: typeof Schema.String;
2000
+ /** Optional human-readable column description. */
2001
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2002
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
2003
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
2004
+ /** If true, rows may omit a value for this column. */
2005
+ optional: typeof Schema.Boolean;
2006
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
2007
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
2008
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
2009
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
2010
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
2011
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
2012
+ /** Open suggestion list for this column. */
2013
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
2014
+ }>>]>>;
2015
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
2016
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
2017
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
2018
+ name: typeof Schema.String;
2019
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
2020
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
2021
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
2022
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2023
+ }>>]>>;
2024
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
2025
+ }>, Schema.Struct<{
2026
+ /** The unique identifier for this object. */
2027
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2028
+ /** A short, human-readable label of this object. */
2029
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2030
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2031
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2032
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2033
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1058
2034
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1059
2035
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
1060
2036
  top: typeof Schema.Number;
1061
2037
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1062
2038
  left: typeof Schema.Number;
1063
2039
  }>]>>;
2040
+ /** Must be ``integer`` or ``int``. */
2041
+ type: Schema.Literal<["integer", "int"]>;
2042
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2043
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2044
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2045
+ }>, Schema.Struct<{
2046
+ /** The unique identifier for this object. */
2047
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2048
+ /** A short, human-readable label of this object. */
2049
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2050
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2051
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2052
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1064
2053
  default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1065
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
2054
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2055
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2056
+ top: typeof Schema.Number;
2057
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2058
+ left: typeof Schema.Number;
2059
+ }>]>>;
2060
+ /** Must be ``float``. */
2061
+ type: Schema.Literal<["float"]>;
2062
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2063
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2064
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2065
+ }>, Schema.Struct<{
1066
2066
  /** The unique identifier for this object. */
1067
2067
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1068
2068
  /** A short, human-readable label of this object. */
1069
2069
  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1070
2070
  /** A documentation string for this object, or an array of strings which should be concatenated. */
1071
2071
  doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1072
- /** Specify valid types of data that may be assigned to this parameter. */
1073
- type: Schema.optional<Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>, typeof Schema.Null, Schema.Array$<Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>>]>>;
1074
- /** If set to true, `WorkflowInputParameter` is not required to submit the workflow. */
2072
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2073
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2074
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2075
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2076
+ top: typeof Schema.Number;
2077
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2078
+ left: typeof Schema.Number;
2079
+ }>]>>;
2080
+ /** Must be ``text`` or ``string``. */
2081
+ type: Schema.Literal<["text", "string"]>;
2082
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
2083
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
2084
+ /** Machine value submitted to the connected tool input. */
2085
+ value: typeof Schema.String;
2086
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
2087
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2088
+ }>]>>]>>;
2089
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
2090
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
2091
+ /** Machine value submitted to the connected tool input. */
2092
+ value: typeof Schema.String;
2093
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
2094
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2095
+ }>]>>]>>;
2096
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
2097
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
2098
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2099
+ }>, Schema.Struct<{
2100
+ /** The unique identifier for this object. */
2101
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2102
+ /** A short, human-readable label of this object. */
2103
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2104
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2105
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2106
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2107
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2108
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2109
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2110
+ top: typeof Schema.Number;
2111
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2112
+ left: typeof Schema.Number;
2113
+ }>]>>;
2114
+ /** Must be ``boolean``. */
2115
+ type: Schema.Literal<["boolean"]>;
2116
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2117
+ }>]>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
2118
+ /** The unique identifier for this object. */
2119
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2120
+ /** A short, human-readable label of this object. */
2121
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2122
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2123
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2124
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2125
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2126
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2127
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2128
+ top: typeof Schema.Number;
2129
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2130
+ left: typeof Schema.Number;
2131
+ }>]>>;
2132
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
1075
2133
  optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1076
- /** Specify datatype extension for valid input datasets. */
2134
+ /** Specify valid types of data that may be assigned to this parameter. */
2135
+ type: Schema.optional<Schema.Union<[Schema.Literal<["data", "File"]>, typeof Schema.Null]>>;
1077
2136
  format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
2137
+ }>, Schema.Struct<{
2138
+ /** The unique identifier for this object. */
2139
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2140
+ /** A short, human-readable label of this object. */
2141
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2142
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2143
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2144
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2145
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2146
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2147
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2148
+ top: typeof Schema.Number;
2149
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2150
+ left: typeof Schema.Number;
2151
+ }>]>>;
2152
+ /** Controls whether Galaxy allows invocation of the workflow without a user-supplied value for this input. If ``true``, the input may be omitted at invocation time. ``optional`` and ``default`` are in... */
2153
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2154
+ /** Must be ``collection``. */
2155
+ type: Schema.Literal<["collection"]>;
1078
2156
  /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
1079
2157
  collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2158
+ /** Column schema for sample-sheet collection inputs. Only meaningful when `collection_type` begins with `sample_sheet` - cross-field validation is applied in the pydantic post-validator. */
2159
+ column_definitions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
2160
+ /** Column name. Must not contain special characters (matches `^[\w\-_ \?]*$`). */
2161
+ name: typeof Schema.String;
2162
+ /** Optional human-readable column description. */
2163
+ description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2164
+ /** Value type for this column. One of `string`, `int`, `float`, `boolean`, or `element_identifier`. Mirrors Galaxy's runtime `SampleSheetColumnType`. */
2165
+ type: Schema.Literal<["string", "int", "float", "boolean", "element_identifier"]>;
2166
+ /** If true, rows may omit a value for this column. */
2167
+ optional: typeof Schema.Boolean;
2168
+ /** Default value used when a row omits this column. Type must be compatible with `type` - validated by the pydantic post-validator. */
2169
+ default_value: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, typeof Schema.Number, typeof Schema.Boolean]>>;
2170
+ /** Galaxy-style parameter validators. Modelled as opaque records here - full validator schema lives in galaxy.tool_util_models. */
2171
+ validators: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.Unknown>]>>;
2172
+ /** Closed set of permitted values for this column. Item type must be compatible with the column `type` (post-validated). */
2173
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
2174
+ /** Open suggestion list for this column. */
2175
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number, typeof Schema.Number, typeof Schema.Boolean]>>]>>;
2176
+ }>>]>>;
2177
+ /** Field schema for `record` collection inputs. Only meaningful when `collection_type` contains `record` (e.g. `record`, `list:record`, `sample_sheet:record`). */
2178
+ fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Struct<{
2179
+ /** Field name. Must equal the corresponding element identifier in the materialized record collection. */
2180
+ name: typeof Schema.String;
2181
+ /** Field value type. A subset of the CWL primitive types: `File`, `null`, `boolean`, `int`, `float`, `string`. May be a list to express a union (e.g. `["File", "null"]` for an optional file). */
2182
+ type: Schema.Union<[Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>, Schema.Array$<Schema.Literal<["File", "null", "boolean", "int", "float", "string"]>>]>;
2183
+ /** Optional Galaxy datatype hint for `File`-typed fields. */
2184
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2185
+ }>>]>>;
2186
+ format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
2187
+ }>, Schema.Struct<{
2188
+ /** The unique identifier for this object. */
2189
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2190
+ /** A short, human-readable label of this object. */
2191
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2192
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2193
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2194
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2195
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2196
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2197
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2198
+ top: typeof Schema.Number;
2199
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2200
+ left: typeof Schema.Number;
2201
+ }>]>>;
2202
+ /** Must be ``integer`` or ``int``. */
2203
+ type: Schema.Literal<["integer", "int"]>;
2204
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2205
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2206
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2207
+ }>, Schema.Struct<{
2208
+ /** The unique identifier for this object. */
2209
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2210
+ /** A short, human-readable label of this object. */
2211
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2212
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2213
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2214
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2215
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2216
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2217
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2218
+ top: typeof Schema.Number;
2219
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2220
+ left: typeof Schema.Number;
2221
+ }>]>>;
2222
+ /** Must be ``float``. */
2223
+ type: Schema.Literal<["float"]>;
2224
+ min: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2225
+ max: Schema.optional<Schema.Union<[typeof Schema.Number, typeof Schema.Null]>>;
2226
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2227
+ }>, Schema.Struct<{
2228
+ /** The unique identifier for this object. */
2229
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2230
+ /** A short, human-readable label of this object. */
2231
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2232
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2233
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2234
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
2235
+ default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1080
2236
  position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1081
2237
  /** Relative vertical position of the step's node when rendered in the workflow editor. */
1082
2238
  top: typeof Schema.Number;
1083
2239
  /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1084
2240
  left: typeof Schema.Number;
1085
2241
  }>]>>;
2242
+ /** Must be ``text`` or ``string``. */
2243
+ type: Schema.Literal<["text", "string"]>;
2244
+ /** Closed set of permitted values. When present, Galaxy renders the runtime input as a select. Items may be plain strings or `{value, label}` records. */
2245
+ restrictions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
2246
+ /** Machine value submitted to the connected tool input. */
2247
+ value: typeof Schema.String;
2248
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
2249
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2250
+ }>]>>]>>;
2251
+ /** Open suggestion list. Galaxy still treats the input as text but offers these as suggestions. */
2252
+ suggestions: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, Schema.Struct<{
2253
+ /** Machine value submitted to the connected tool input. */
2254
+ value: typeof Schema.String;
2255
+ /** Human label shown in Galaxy. Defaults to `value` when omitted. */
2256
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2257
+ }>]>>]>>;
2258
+ /** Ask Galaxy to derive valid choices from connected tool or subworkflow select inputs at runtime. Falls back to free text when derivation fails. */
2259
+ restrictOnConnections: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
2260
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
2261
+ }>, Schema.Struct<{
2262
+ /** The unique identifier for this object. */
2263
+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2264
+ /** A short, human-readable label of this object. */
2265
+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
2266
+ /** A documentation string for this object, or an array of strings which should be concatenated. */
2267
+ doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
2268
+ /** The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before eva... */
1086
2269
  default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
2270
+ position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
2271
+ /** Relative vertical position of the step's node when rendered in the workflow editor. */
2272
+ top: typeof Schema.Number;
2273
+ /** Relative horizontal position of the step's node when rendered in the workflow editor. */
2274
+ left: typeof Schema.Number;
2275
+ }>]>>;
2276
+ /** Must be ``boolean``. */
2277
+ type: Schema.Literal<["boolean"]>;
2278
+ optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1087
2279
  }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
1088
2280
  outputs: Schema.Union<[Schema.Array$<Schema.Struct<{
1089
2281
  /** The unique identifier for this object. */
@@ -1137,4 +2329,10 @@ export declare const WorkflowStepSchema: Schema.Struct<{
1137
2329
  id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1138
2330
  }>;
1139
2331
  export type WorkflowStep = typeof WorkflowStepSchema.Type;
2332
+ export declare function isWorkflowDataParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowDataParameter;
2333
+ export declare function isWorkflowCollectionParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowCollectionParameter;
2334
+ export declare function isWorkflowIntegerParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowIntegerParameter;
2335
+ export declare function isWorkflowTextParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowTextParameter;
2336
+ export declare function isWorkflowFloatParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowFloatParameter;
2337
+ export declare function isWorkflowBooleanParameter(v: WorkflowDataParameter | WorkflowCollectionParameter | WorkflowIntegerParameter | WorkflowTextParameter | WorkflowFloatParameter | WorkflowBooleanParameter): v is WorkflowBooleanParameter;
1140
2338
  //# sourceMappingURL=gxformat2.effect.d.ts.map