Provide more field annotations (0e13bace) · Commits · NDIP / Galaxy

client/src/api/schema/schema.ts

+238 −55

Original line number	Diff line number	Diff line
		@@ -6617,10 +6617,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -6771,10 +6775,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -7149,10 +7157,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -7341,10 +7353,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -7384,10 +7400,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -8439,7 +8459,10 @@ export interface components {
		};
		/** CwlBooleanParameterModel */
		CwlBooleanParameterModel: {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8466,10 +8489,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -8498,10 +8525,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -8514,7 +8545,10 @@ export interface components {
		};
		/** CwlFloatParameterModel */
		CwlFloatParameterModel: {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8525,7 +8559,10 @@ export interface components {
		};
		/** CwlIntegerParameterModel */
		CwlIntegerParameterModel: {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8536,7 +8573,10 @@ export interface components {
		};
		/** CwlNullParameterModel */
		CwlNullParameterModel: {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8547,7 +8587,10 @@ export interface components {
		};
		/** CwlStringParameterModel */
		CwlStringParameterModel: {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8558,7 +8601,10 @@ export interface components {
		};
		/** CwlUnionParameterModel */
		"CwlUnionParameterModel-Input": {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8580,7 +8626,10 @@ export interface components {
		};
		/** CwlUnionParameterModel */
		"CwlUnionParameterModel-Output": {
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Parameter Type
		@@ -8714,10 +8763,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -8757,10 +8810,14 @@ export interface components {
		label?: string \| null;
		/** Multiple */
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -8840,6 +8897,7 @@ export interface components {
		argument?: string \| null;
		/**
		* Extensions
		* @description Limit inputs to datasets with these extensions. Use 'data' to allow all input datasets.
		* @default [
		* "data"
		* ]
		@@ -8865,13 +8923,18 @@ export interface components {
		min?: number \| null;
		/**
		* Multiple
		* @description Allow multiple values to be selected.
		* @default false
		*/
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -9574,10 +9637,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -9693,10 +9760,14 @@ export interface components {
		label?: string \| null;
		/** Multiple */
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -9739,10 +9810,14 @@ export interface components {
		label?: string \| null;
		/** Multiple */
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -10729,10 +10804,14 @@ export interface components {
		max?: number \| null;
		/** Min */
		min?: number \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -10945,10 +11024,14 @@ export interface components {
		label?: string \| null;
		/** Multiple */
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -11091,10 +11174,14 @@ export interface components {
		label?: string \| null;
		/** Multiple */
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -12722,10 +12809,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -13200,7 +13291,10 @@ export interface components {
		};
		/** IncomingToolOutputCollection */
		"IncomingToolOutputCollection-Input": {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden?: boolean \| null;
		/** Label */
		label?: string \| null;
		@@ -13218,7 +13312,10 @@ export interface components {
		};
		/** IncomingToolOutputCollection */
		"IncomingToolOutputCollection-Output": {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden?: boolean \| null;
		/** Label */
		label?: string \| null;
		@@ -13252,7 +13349,10 @@ export interface components {
		format_source?: string \| null;
		/** From Work Dir */
		from_work_dir?: string \| null;
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden?: boolean \| null;
		/** Label */
		label?: string \| null;
		@@ -13533,7 +13633,10 @@ export interface components {
		max?: number \| null;
		/** Min */
		min?: number \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/** Optional */
		optional: boolean;
		@@ -17531,10 +17634,14 @@ export interface components {
		max?: number \| null;
		/** Min */
		min?: number \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -17602,10 +17709,14 @@ export interface components {
		max?: number \| null;
		/** Min */
		min?: number \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -17813,10 +17924,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -17872,10 +17987,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -17939,10 +18058,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -18011,10 +18134,14 @@ export interface components {
		* @default false
		*/
		multiple: boolean;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -19116,10 +19243,14 @@ export interface components {
		is_dynamic: boolean;
		/** Label */
		label?: string \| null;
		/** Name */
		/**
		* Name
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/**
		* Optional
		* @description If `false`, parameter must have a value.
		* @default false
		*/
		optional: boolean;
		@@ -19229,7 +19360,10 @@ export interface components {
		};
		/** ToolOutputBoolean */
		ToolOutputBoolean: {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden: unknown;
		/** Label */
		label?: string \| null;
		@@ -19264,7 +19398,10 @@ export interface components {
		};
		/** ToolOutputFloat */
		ToolOutputFloat: {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden: unknown;
		/** Label */
		label?: string \| null;
		@@ -19281,7 +19418,10 @@ export interface components {
		};
		/** ToolOutputInteger */
		ToolOutputInteger: {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden: unknown;
		/** Label */
		label?: string \| null;
		@@ -19298,7 +19438,10 @@ export interface components {
		};
		/** ToolOutputText */
		ToolOutputText: {
		/** Hidden */
		/**
		* Hidden
		* @description If true, the output will not be shown in the history.
		*/
		hidden: unknown;
		/** Label */
		label?: string \| null;
		@@ -20392,25 +20535,41 @@ export interface components {
		* @enum {string}
		*/
		class: "GalaxyUserTool";
		/** Container */
		/**
		* Container
		* @description Container image to use for this tool.
		*/
		container: string;
		/** Description */
		/**
		* Description
		* @description The description is displayed in the tool menu immediately following the hyperlink for the tool.
		*/
		description?: string \| null;
		/** Edam Operations */
		edam_operations?: string[] \| null;
		/** Edam Topics */
		edam_topics?: string[] \| null;
		/** @description Help text shown below the tool interface. */
		help?: components["schemas"]["HelpContent"] \| null;
		/** Id */
		id: string \| null;
		/**
		* Id
		* @description Unique identifier for the tool. Should be all lower-case and should not include whitespace.
		*/
		id: string;
		/**
		* Inputs
		* @default []
		*/
		inputs: components["schemas"]["GalaxyToolParameterModel-Input"][];
		/** License */
		/**
		* License
		* @description A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.
		*/
		license?: string \| null;
		/** Name */
		/**
		* Name
		* @description The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.
		*/
		name: string;
		/**
		* Outputs
		@@ -20426,6 +20585,7 @@ export interface components {
		)[];
		/**
		* Requirements
		* @description A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.
		* @default []
		*/
		requirements:
		@@ -20440,8 +20600,11 @@ export interface components {
		* @description A string that contains the command to be executed. Parameters can be referenced inside $().
		*/
		shell_command: string;
		/** Version */
		version: string \| null;
		/**
		* Version
		* @description Version for the tool.
		*/
		version: string;
		/** Xrefs */
		xrefs?: components["schemas"]["XrefDict"][] \| null;
		};
		@@ -20454,25 +20617,41 @@ export interface components {
		* @constant
		*/
		class: "GalaxyUserTool";
		/** Container */
		/**
		* Container
		* @description Container image to use for this tool.
		*/
		container: string;
		/** Description */
		/**
		* Description
		* @description The description is displayed in the tool menu immediately following the hyperlink for the tool.
		*/
		description?: string \| null;
		/** Edam Operations */
		edam_operations?: string[] \| null;
		/** Edam Topics */
		edam_topics?: string[] \| null;
		/** @description Help text shown below the tool interface. */
		help?: components["schemas"]["HelpContent"] \| null;
		/** Id */
		id: string \| null;
		/**
		* Id
		* @description Unique identifier for the tool. Should be all lower-case and should not include whitespace.
		*/
		id: string;
		/**
		* Inputs
		* @default []
		*/
		inputs: components["schemas"]["GalaxyToolParameterModel-Output"][];
		/** License */
		/**
		* License
		* @description A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.
		*/
		license?: string \| null;
		/** Name */
		/**
		* Name
		* @description The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.
		*/
		name: string;
		/**
		* Outputs
		@@ -20488,6 +20667,7 @@ export interface components {
		)[];
		/**
		* Requirements
		* @description A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.
		* @default []
		*/
		requirements:
		@@ -20502,8 +20682,11 @@ export interface components {
		* @description A string that contains the command to be executed. Parameters can be referenced inside $().
		*/
		shell_command: string;
		/** Version */
		version: string \| null;
		/**
		* Version
		* @description Version for the tool.
		*/
		version: string;
		/** Xrefs */
		xrefs?: components["schemas"]["XrefDict"][] \| null;
		};

client/src/components/Tool/ToolSourceSchema.json

+1 −1

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client/src/components/Tool/YamlJs.ts

+39 −12

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lib/galaxy/tool_util/xsd/galaxy.xsd

+4 −4

Original line number	Diff line number	Diff line
		@@ -204,7 +204,7 @@ for the list of behavior changes associated with profile versions.
		<xs:annotation>
		<xs:documentation xml:lang="en">This string specifies any full URI or a
		a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool
		wrapper. The tool wrapper version can be indepedent of the underlying tool. This
		wrapper. The tool wrapper version can be independent of the underlying tool. This
		license covers the tool XML and associated scripts shipped with the tool.

		This is interpreted as [schema.org/license](https://schema.org/license) property.

lib/galaxy/tool_util_models/init.py

+39 −8

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