@galaxy-tool-util/schema 0.1.0 → 0.2.0

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Files changed (81) hide show
  1. package/LICENSE +21 -0
  2. package/dist/index.d.ts +14 -0
  3. package/dist/index.d.ts.map +1 -1
  4. package/dist/index.js +14 -0
  5. package/dist/index.js.map +1 -1
  6. package/dist/workflow/clean.d.ts +27 -0
  7. package/dist/workflow/clean.d.ts.map +1 -1
  8. package/dist/workflow/clean.js +29 -0
  9. package/dist/workflow/clean.js.map +1 -1
  10. package/dist/workflow/coercions.d.ts +22 -0
  11. package/dist/workflow/coercions.d.ts.map +1 -0
  12. package/dist/workflow/coercions.js +67 -0
  13. package/dist/workflow/coercions.js.map +1 -0
  14. package/dist/workflow/index.d.ts +6 -1
  15. package/dist/workflow/index.d.ts.map +1 -1
  16. package/dist/workflow/index.js +6 -1
  17. package/dist/workflow/index.js.map +1 -1
  18. package/dist/workflow/normalized/index.d.ts +5 -2
  19. package/dist/workflow/normalized/index.d.ts.map +1 -1
  20. package/dist/workflow/normalized/index.js +2 -0
  21. package/dist/workflow/normalized/index.js.map +1 -1
  22. package/dist/workflow/normalized/stateful-runner.d.ts +82 -0
  23. package/dist/workflow/normalized/stateful-runner.d.ts.map +1 -0
  24. package/dist/workflow/normalized/stateful-runner.js +122 -0
  25. package/dist/workflow/normalized/stateful-runner.js.map +1 -0
  26. package/dist/workflow/normalized/toFormat2.d.ts +19 -1
  27. package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
  28. package/dist/workflow/normalized/toFormat2.js +47 -16
  29. package/dist/workflow/normalized/toFormat2.js.map +1 -1
  30. package/dist/workflow/normalized/toFormat2Stateful.d.ts +30 -0
  31. package/dist/workflow/normalized/toFormat2Stateful.d.ts.map +1 -0
  32. package/dist/workflow/normalized/toFormat2Stateful.js +58 -0
  33. package/dist/workflow/normalized/toFormat2Stateful.js.map +1 -0
  34. package/dist/workflow/normalized/toNative.d.ts +10 -1
  35. package/dist/workflow/normalized/toNative.d.ts.map +1 -1
  36. package/dist/workflow/normalized/toNative.js +24 -8
  37. package/dist/workflow/normalized/toNative.js.map +1 -1
  38. package/dist/workflow/normalized/toNativeStateful.d.ts +31 -0
  39. package/dist/workflow/normalized/toNativeStateful.d.ts.map +1 -0
  40. package/dist/workflow/normalized/toNativeStateful.js +55 -0
  41. package/dist/workflow/normalized/toNativeStateful.js.map +1 -0
  42. package/dist/workflow/precheck.d.ts +54 -0
  43. package/dist/workflow/precheck.d.ts.map +1 -0
  44. package/dist/workflow/precheck.js +91 -0
  45. package/dist/workflow/precheck.js.map +1 -0
  46. package/dist/workflow/raw/gxformat2.effect.d.ts +108 -332
  47. package/dist/workflow/raw/gxformat2.effect.d.ts.map +1 -1
  48. package/dist/workflow/raw/gxformat2.effect.js +106 -94
  49. package/dist/workflow/raw/gxformat2.effect.js.map +1 -1
  50. package/dist/workflow/raw/native.effect.d.ts +30 -177
  51. package/dist/workflow/raw/native.effect.d.ts.map +1 -1
  52. package/dist/workflow/raw/native.effect.js +43 -31
  53. package/dist/workflow/raw/native.effect.js.map +1 -1
  54. package/dist/workflow/roundtrip.d.ts +54 -0
  55. package/dist/workflow/roundtrip.d.ts.map +1 -0
  56. package/dist/workflow/roundtrip.js +516 -0
  57. package/dist/workflow/roundtrip.js.map +1 -0
  58. package/dist/workflow/runtime-markers.d.ts +20 -0
  59. package/dist/workflow/runtime-markers.d.ts.map +1 -0
  60. package/dist/workflow/runtime-markers.js +26 -0
  61. package/dist/workflow/runtime-markers.js.map +1 -0
  62. package/dist/workflow/stale-keys.d.ts +16 -0
  63. package/dist/workflow/stale-keys.d.ts.map +1 -0
  64. package/dist/workflow/stale-keys.js +43 -0
  65. package/dist/workflow/stale-keys.js.map +1 -0
  66. package/dist/workflow/state-merge.d.ts.map +1 -1
  67. package/dist/workflow/state-merge.js +5 -22
  68. package/dist/workflow/state-merge.js.map +1 -1
  69. package/dist/workflow/stateful-convert.d.ts +47 -0
  70. package/dist/workflow/stateful-convert.d.ts.map +1 -0
  71. package/dist/workflow/stateful-convert.js +151 -0
  72. package/dist/workflow/stateful-convert.js.map +1 -0
  73. package/dist/workflow/stateful-validate.d.ts +46 -0
  74. package/dist/workflow/stateful-validate.d.ts.map +1 -0
  75. package/dist/workflow/stateful-validate.js +96 -0
  76. package/dist/workflow/stateful-validate.js.map +1 -0
  77. package/dist/workflow/walker.d.ts +53 -0
  78. package/dist/workflow/walker.d.ts.map +1 -0
  79. package/dist/workflow/walker.js +189 -0
  80. package/dist/workflow/walker.js.map +1 -0
  81. package/package.json +18 -14
@@ -386,27 +386,6 @@ export declare const ReferencesToolSchema: Schema.Struct<{
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  tool_version: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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  export type ReferencesTool = typeof ReferencesToolSchema.Type;
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- /**
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- * Associate an output parameter of the underlying process with a workflow
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- parameter. The workflow parameter (given in the `id` field) be may be used
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- as a `source` to connect with input parameters of other workflow steps, or
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- with an output parameter of the process.
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-
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- A unique identifier for this workflow output parameter. This is
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- the identifier to use in the `source` field of `WorkflowStepInput`
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- to connect the output value to downstream parameters.
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- */
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- export declare const WorkflowStepOutputSchema: Schema.Struct<{
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- add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
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- change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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- hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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- remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
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- rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
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- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- }>;
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- export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
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  export declare const SinkSchema: Schema.Struct<{
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  /** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
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  source: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
@@ -424,14 +403,48 @@ export declare const WorkflowStepInputSchema: Schema.Struct<{
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  }>;
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  export type WorkflowStepInput = typeof WorkflowStepInputSchema.Type;
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  /**
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- * Definition of an invocation report for this workflow. Currently the only
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- field is 'markdown'.
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+ * Base fields shared by all creator types, corresponding to schema.org
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+ Thing properties common to both Person and Organization.
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  */
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- export declare const ReportSchema: Schema.Struct<{
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- /** Galaxy flavored Markdown to define an invocation report. */
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- markdown: typeof Schema.String;
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+ export declare const BaseCreatorSchema: Schema.Struct<{
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+ /** Full name of the person or organization. */
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+ name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID. */
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+ identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Website or profile URL. */
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+ url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Email address. May include a ``mailto:`` prefix. */
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+ email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** URL to an image or avatar. */
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+ image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Physical or mailing address. */
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+ address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** An alternate name or alias. */
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+ alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Telephone number. */
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+ telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Fax number. */
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+ faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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- export type Report = typeof ReportSchema.Type;
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+ export type BaseCreator = typeof BaseCreatorSchema.Type;
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+ /**
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+ * An organization that created or contributed to the workflow.
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+ Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
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+ */
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+ export declare const CreatorOrganizationSchema: Schema.Struct<{
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+ /** Creator type discriminator (``Organization``). */
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+ class: Schema.Literal<["Organization"]>;
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+ name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ }>;
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+ export type CreatorOrganization = typeof CreatorOrganizationSchema.Type;
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  /**
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  * Base fields shared by all comment types.
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  */
@@ -446,26 +459,6 @@ export declare const BaseCommentSchema: Schema.Struct<{
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  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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  export type BaseComment = typeof BaseCommentSchema.Type;
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- /**
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- * A plain text annotation in the workflow editor.
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- */
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- export declare const TextCommentSchema: Schema.Struct<{
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- /** Comment type (``text``). */
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- type: Schema.Literal<["text"]>;
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- /** The text content. */
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- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Whether the text is displayed in bold. */
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- bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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- /** Whether the text is displayed in italic. */
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- italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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- /** Font size of the text. */
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- text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
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- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- }>;
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- export type TextComment = typeof TextCommentSchema.Type;
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  /**
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  * A Markdown-rendered annotation in the workflow editor.
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  */
@@ -481,46 +474,52 @@ export declare const MarkdownCommentSchema: Schema.Struct<{
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  }>;
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  export type MarkdownComment = typeof MarkdownCommentSchema.Type;
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  /**
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- * A freehand drawn line on the editor canvas.
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+ * Definition of an invocation report for this workflow. Currently the only
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+ field is 'markdown'.
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  */
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- export declare const FreehandCommentSchema: Schema.Struct<{
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- /** Comment type (``freehand``). */
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- type: Schema.Literal<["freehand"]>;
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- /** Line thickness. */
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- thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
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- /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
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- line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
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+ export declare const ReportSchema: Schema.Struct<{
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+ /** Galaxy flavored Markdown to define an invocation report. */
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+ markdown: typeof Schema.String;
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+ }>;
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+ export type Report = typeof ReportSchema.Type;
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+ /**
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+ * A rectangular grouping box that visually contains steps and other comments.
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+ */
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+ export declare const FrameCommentSchema: Schema.Struct<{
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+ /** Comment type (``frame``). */
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+ type: Schema.Literal<["frame"]>;
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+ /** Title displayed on the frame header. */
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+ title: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Step labels or indices contained within this frame. */
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+ contains_steps: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
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+ /** Comment labels or indices contained within this frame. */
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+ contains_comments: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
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  position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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  size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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  color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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- export type FreehandComment = typeof FreehandCommentSchema.Type;
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+ export type FrameComment = typeof FrameCommentSchema.Type;
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  /**
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- * Base fields shared by all creator types, corresponding to schema.org
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- Thing properties common to both Person and Organization.
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+ * A plain text annotation in the workflow editor.
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  */
503
- export declare const BaseCreatorSchema: Schema.Struct<{
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- /** Full name of the person or organization. */
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- name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID. */
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- identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Website or profile URL. */
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- url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Email address. May include a ``mailto:`` prefix. */
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- email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** URL to an image or avatar. */
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- image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Physical or mailing address. */
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- address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** An alternate name or alias. */
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- alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Telephone number. */
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- telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Fax number. */
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- faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ export declare const TextCommentSchema: Schema.Struct<{
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+ /** Comment type (``text``). */
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+ type: Schema.Literal<["text"]>;
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+ /** The text content. */
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+ text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ /** Whether the text is displayed in bold. */
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+ bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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+ /** Whether the text is displayed in italic. */
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+ italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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+ /** Font size of the text. */
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+ text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
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+ position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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+ size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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+ color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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- export type BaseCreator = typeof BaseCreatorSchema.Type;
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+ export type TextComment = typeof TextCommentSchema.Type;
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  /**
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  * A person who created or contributed to the workflow.
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  Corresponds to a `schema.org Person <https://schema.org/Person>`_.
@@ -550,41 +549,21 @@ export declare const CreatorPersonSchema: Schema.Struct<{
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  }>;
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  export type CreatorPerson = typeof CreatorPersonSchema.Type;
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  /**
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- * A rectangular grouping box that visually contains steps and other comments.
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+ * A freehand drawn line on the editor canvas.
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  */
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- export declare const FrameCommentSchema: Schema.Struct<{
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- /** Comment type (``frame``). */
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- type: Schema.Literal<["frame"]>;
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- /** Title displayed on the frame header. */
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- title: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** Step labels or indices contained within this frame. */
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- contains_steps: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
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- /** Comment labels or indices contained within this frame. */
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- contains_comments: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
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+ export declare const FreehandCommentSchema: Schema.Struct<{
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+ /** Comment type (``freehand``). */
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+ type: Schema.Literal<["freehand"]>;
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+ /** Line thickness. */
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+ thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
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+ /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
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+ line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
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  position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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  size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
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  color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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  }>;
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- export type FrameComment = typeof FrameCommentSchema.Type;
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- /**
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- * An organization that created or contributed to the workflow.
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- Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
573
- */
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- export declare const CreatorOrganizationSchema: Schema.Struct<{
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- /** Creator type discriminator (``Organization``). */
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- class: Schema.Literal<["Organization"]>;
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- name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- }>;
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- export type CreatorOrganization = typeof CreatorOrganizationSchema.Type;
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+ export type FreehandComment = typeof FreehandCommentSchema.Type;
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  /**
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  * A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable
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  on a Galaxy server that includes the contained tool definitions.
@@ -825,6 +804,27 @@ export declare const GalaxyWorkflowSchema: Schema.Struct<{
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  }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
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  }>;
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  export type GalaxyWorkflow = typeof GalaxyWorkflowSchema.Type;
807
+ /**
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+ * Associate an output parameter of the underlying process with a workflow
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+ parameter. The workflow parameter (given in the `id` field) be may be used
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+ as a `source` to connect with input parameters of other workflow steps, or
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+ with an output parameter of the process.
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+
813
+ A unique identifier for this workflow output parameter. This is
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+ the identifier to use in the `source` field of `WorkflowStepInput`
815
+ to connect the output value to downstream parameters.
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+ */
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+ export declare const WorkflowStepOutputSchema: Schema.Struct<{
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+ add_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
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+ change_datatype: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ delete_intermediate_datasets: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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+ hide: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
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+ remove_tags: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
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+ rename: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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+ set_columns: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
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+ id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
826
+ }>;
827
+ export type WorkflowStepOutput = typeof WorkflowStepOutputSchema.Type;
828
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  /**
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  * This represents a non-input step a Galaxy Workflow.
830
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@@ -884,231 +884,7 @@ export declare const WorkflowStepSchema: Schema.Struct<{
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  /** Workflow step module's type (defaults to 'tool'). */
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  type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["tool", "subworkflow", "pause", "pick_value"]>]>>;
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  /** Specifies a subworkflow to run. May be an inline workflow definition, a URL string, or an @import reference dict. */
887
- run: Schema.optional<Schema.Union<[Schema.Struct<{
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- /** The unique identifier for this object. */
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- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
890
- class: Schema.Literal<["GalaxyWorkflow"]>;
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- /** A short, human-readable label of this object. */
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- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
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- /** 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$<typeof Schema.String>]>>;
895
- /** The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled. */
896
- steps: Schema.Union<[Schema.Array$<Schema.suspend<any, any, never>>, Schema.Record$<typeof Schema.String, Schema.suspend<any, any, never>>]>;
897
- /** Workflow invocation report template. */
898
- report: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
899
- /** Galaxy flavored Markdown to define an invocation report. */
900
- markdown: typeof Schema.String;
901
- }>]>>;
902
- /** Tags for the workflow. */
903
- tags: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.String>, typeof Schema.Null]>>;
904
- /** Visual annotations for the workflow editor canvas. Comments are non-functional and do not affect workflow execution. May be specified as a list or as a mapping keyed by label. */
905
- comments: Schema.optional<Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
906
- /** Comment type (``text``). */
907
- type: Schema.Literal<["text"]>;
908
- /** The text content. */
909
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
910
- /** Whether the text is displayed in bold. */
911
- bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
912
- /** Whether the text is displayed in italic. */
913
- italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
914
- /** Font size of the text. */
915
- text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
916
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
917
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
918
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
919
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
920
- }>, Schema.Struct<{
921
- /** Comment type (``markdown``). */
922
- type: Schema.Literal<["markdown"]>;
923
- /** Markdown content. */
924
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
925
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
926
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
927
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
928
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
929
- }>, Schema.Struct<{
930
- /** Comment type (``frame``). */
931
- type: Schema.Literal<["frame"]>;
932
- /** Title displayed on the frame header. */
933
- title: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
934
- /** Step labels or indices contained within this frame. */
935
- contains_steps: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
936
- /** Comment labels or indices contained within this frame. */
937
- contains_comments: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
938
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
939
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
940
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
941
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
942
- }>, Schema.Struct<{
943
- /** Comment type (``freehand``). */
944
- type: Schema.Literal<["freehand"]>;
945
- /** Line thickness. */
946
- thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
947
- /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
948
- line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
949
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
950
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
951
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
952
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
953
- }>]>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
954
- /** Comment type (``text``). */
955
- type: Schema.Literal<["text"]>;
956
- /** The text content. */
957
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
958
- /** Whether the text is displayed in bold. */
959
- bold: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
960
- /** Whether the text is displayed in italic. */
961
- italic: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Boolean]>>;
962
- /** Font size of the text. */
963
- text_size: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
964
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
965
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
966
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
967
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
968
- }>, Schema.Struct<{
969
- /** Comment type (``markdown``). */
970
- type: Schema.Literal<["markdown"]>;
971
- /** Markdown content. */
972
- text: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
973
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
974
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
975
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
976
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
977
- }>, Schema.Struct<{
978
- /** Comment type (``frame``). */
979
- type: Schema.Literal<["frame"]>;
980
- /** Title displayed on the frame header. */
981
- title: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
982
- /** Step labels or indices contained within this frame. */
983
- contains_steps: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
984
- /** Comment labels or indices contained within this frame. */
985
- contains_comments: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.Union<[typeof Schema.String, typeof Schema.Number]>>]>>;
986
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
987
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
988
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
989
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
990
- }>, Schema.Struct<{
991
- /** Comment type (``freehand``). */
992
- type: Schema.Literal<["freehand"]>;
993
- /** Line thickness. */
994
- thickness: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Number]>>;
995
- /** Array of ``[x, y]`` coordinate pairs defining the freehand line path. */
996
- line: Schema.optional<Schema.Union<[Schema.Array$<Schema.Array$<typeof Schema.Number>>, typeof Schema.Null]>>;
997
- position: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
998
- size: Schema.optional<Schema.Union<[Schema.Array$<typeof Schema.Number>, typeof Schema.Null]>>;
999
- color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1000
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1001
- }>]>>, typeof Schema.Null]>>;
1002
- /** Workflow creators. Can be schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entities. */
1003
- creator: Schema.optional<Schema.Union<[Schema.Array$<Schema.Union<[Schema.Struct<{
1004
- /** Creator type discriminator (``Person``). */
1005
- class: Schema.Literal<["Person"]>;
1006
- /** Given (first) name. */
1007
- givenName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1008
- /** Family (last) name. */
1009
- familyName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1010
- /** Honorific prefix (e.g. ``Dr``, ``Prof``). */
1011
- honorificPrefix: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1012
- /** Honorific suffix (e.g. ``M.D.``, ``PhD``). */
1013
- honorificSuffix: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1014
- /** Job title or role. */
1015
- jobTitle: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1016
- name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1017
- identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1018
- url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1019
- email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1020
- image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1021
- address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1022
- alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1023
- telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1024
- faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1025
- }>, Schema.Struct<{
1026
- /** Creator type discriminator (``Organization``). */
1027
- class: Schema.Literal<["Organization"]>;
1028
- name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1029
- identifier: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1030
- url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1031
- email: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1032
- image: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1033
- address: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1034
- alternateName: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1035
- telephone: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1036
- faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1037
- }>]>>, typeof Schema.Null]>>;
1038
- /** Must be a valid license listed at https://spdx.org/licenses/ */
1039
- license: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1040
- /** If listed should correspond to the release of the workflow in its source reposiory. */
1041
- release: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1042
- uuid: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1043
- inputs: Schema.Union<[Schema.Array$<Schema.Struct<{
1044
- /** The unique identifier for this object. */
1045
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1046
- /** A short, human-readable label of this object. */
1047
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1048
- /** A documentation string for this object, or an array of strings which should be concatenated. */
1049
- 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. */
1053
- optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1054
- /** Specify datatype extension for valid input datasets. */
1055
- format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1056
- /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
1057
- collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1058
- position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1059
- /** Relative vertical position of the step's node when rendered in the workflow editor. */
1060
- top: typeof Schema.Number;
1061
- /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1062
- left: typeof Schema.Number;
1063
- }>]>>;
1064
- default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1065
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
1066
- /** The unique identifier for this object. */
1067
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1068
- /** A short, human-readable label of this object. */
1069
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1070
- /** A documentation string for this object, or an array of strings which should be concatenated. */
1071
- 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. */
1075
- optional: Schema.optional<Schema.Union<[typeof Schema.Boolean, typeof Schema.Null]>>;
1076
- /** Specify datatype extension for valid input datasets. */
1077
- format: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1078
- /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
1079
- collection_type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1080
- position: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Struct<{
1081
- /** Relative vertical position of the step's node when rendered in the workflow editor. */
1082
- top: typeof Schema.Number;
1083
- /** Relative horizontal position of the step's node when rendered in the workflow editor. */
1084
- left: typeof Schema.Number;
1085
- }>]>>;
1086
- default: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.Unknown]>>;
1087
- }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
1088
- outputs: Schema.Union<[Schema.Array$<Schema.Struct<{
1089
- /** The unique identifier for this object. */
1090
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1091
- /** A short, human-readable label of this object. */
1092
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1093
- /** A documentation string for this object, or an array of strings which should be concatenated. */
1094
- doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1095
- /** Specifies workflow parameter that supply the value of to the output parameter. */
1096
- outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1097
- /** Specify valid types of data that may be assigned to this parameter. */
1098
- type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
1099
- }>>, Schema.Record$<typeof Schema.String, Schema.Union<[Schema.Struct<{
1100
- /** The unique identifier for this object. */
1101
- id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1102
- /** A short, human-readable label of this object. */
1103
- label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1104
- /** A documentation string for this object, or an array of strings which should be concatenated. */
1105
- doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
1106
- /** Specifies workflow parameter that supply the value of to the output parameter. */
1107
- outputSource: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
1108
- /** Specify valid types of data that may be assigned to this parameter. */
1109
- type: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string", "integer", "text", "File", "data", "collection"]>]>>;
1110
- }>, typeof Schema.String]>>, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
1111
- }>, typeof Schema.String, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
887
+ run: Schema.optional<Schema.Union<[Schema.suspend<any, any, never>, typeof Schema.String, Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
1112
888
  runtime_inputs: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<typeof Schema.String>]>>;
1113
889
  /** If defined, only run the step when the expression evaluates to `true`. If `false` the step is skipped. A skipped step produces a `null` on each output. Expression should be an ecma5.1 expression. */
1114
890
  when: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
@@ -1 +1 @@
1
- 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