@galaxy-tool-util/schema 1.0.0 → 1.2.0

package/dist/index.d.ts

@@ -39,7 +39,7 @@ type LabelValue, } from "./schema/bundle-types.js";
 export { 
 /** True for gx_select, gx_genomebuild, gx_drill_down — params with an options list. */
 isSelectLikeParam, isBooleanParam, isSectionParam, isRepeatParam, isConditionalParam, } from "./schema/type-guards.js";
-export { ParsedTool, HelpContent, XrefDict, Citation } from "./schema/parsed-tool.js";
+export { ParsedTool, HelpContent, XrefDict, Citation, DiscoverVia, SortKey, SortComp, DatasetCollectionDescription, ToolProvidedMetadataDatasetCollection, FilePatternDatasetCollectionDescription, ToolOutput, ToolOutputDataset, ToolOutputCollectionStructure, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean, parsedToolSchema, } from "./schema/parsed-tool.js";
 export { type GalaxyWorkflow, 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
 GalaxyWorkflowSchema, type NativeGalaxyWorkflow, 
@@ -99,6 +99,14 @@ roundtripValidate, type RoundtripResult, type RoundtripStrictOptions, type StepR
 scanToolState, type LegacyEncodingClassification, type LegacyEncodingHit, type LegacyEncodingScanResult, 
 /** Clean a workflow — strip stale keys, decode legacy tool_state encoding. */
 cleanWorkflow, type CleanWorkflowResult, workflowToMermaid, type MermaidOptions, 
+/** Edge annotation contract (map-over depth + reduction) consumed by mermaid/cytoscape emitters. */
+type EdgeAnnotation, edgeAnnotationKey, 
+/** Build Cytoscape.js elements from a Galaxy workflow. */
+cytoscapeElements, type CytoscapeOptions, 
+/** Flatten cytoscape elements into the list-of-dicts format cytoscape.js consumes. */
+elementsToList, type CytoscapeEdge, type CytoscapeEdgeData, type CytoscapeElements, type CytoscapeLayoutHint, type CytoscapeListItem, type CytoscapeNode, type CytoscapeNodeData, type CytoscapePosition, 
+/** Cross-language layout names + topological position computation. */
+COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, type LayoutName, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, type WorkflowFormat, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */

package/dist/index.d.ts.map

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package/dist/index.js

@@ -24,7 +24,7 @@ collectValidatorTypes, } from "./schema/index.js";
 export { 
 /** True for gx_select, gx_genomebuild, gx_drill_down — params with an options list. */
 isSelectLikeParam, isBooleanParam, isSectionParam, isRepeatParam, isConditionalParam, } from "./schema/type-guards.js";
-export { ParsedTool, HelpContent, XrefDict, Citation } from "./schema/parsed-tool.js";
+export { ParsedTool, HelpContent, XrefDict, Citation, DiscoverVia, SortKey, SortComp, DatasetCollectionDescription, ToolProvidedMetadataDatasetCollection, FilePatternDatasetCollectionDescription, ToolOutput, ToolOutputDataset, ToolOutputCollectionStructure, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean, parsedToolSchema, } from "./schema/parsed-tool.js";
 export { 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
 GalaxyWorkflowSchema, 
@@ -83,7 +83,13 @@ roundtripValidate,
 /** Scan native workflow tool_state for legacy parameter encoding signals. */
 scanToolState, 
 /** Clean a workflow — strip stale keys, decode legacy tool_state encoding. */
-cleanWorkflow, workflowToMermaid, 
+cleanWorkflow, workflowToMermaid, edgeAnnotationKey, 
+/** Build Cytoscape.js elements from a Galaxy workflow. */
+cytoscapeElements, 
+/** Flatten cytoscape elements into the list-of-dicts format cytoscape.js consumes. */
+elementsToList, 
+/** Cross-language layout names + topological position computation. */
+COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO;AACL,0FAA0F;AAC1F,gBAAgB;AAEhB,4CAA4C;AAC5C,qBAAqB;AACrB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,gEAAgE;AAChE,qBAAqB;AACrB,gEAAgE;AAChE,qBAAqB,GACtB,MAAM,mBAAmB,CAAC;AA6B3B,OAAO;AACL,uFAAuF;AACvF,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,aAAa,EACb,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAEtF,OAAO;AAEL,6EAA6E;AAC7E,oBAAoB;AAEpB,oDAAoD;AACpD,0BAA0B;AAC1B,mFAAmF;AACnF,iBAAiB,EACjB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC;AAOjC,wFAAwF;AACxF,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB;AAInB,iEAAiE;AACjE,0BAA0B;AAC1B,oEAAoE;AACpE,oBAAoB;AACpB,oFAAoF;AACpF,uBAAuB;AACvB,kHAAkH;AAClH,qBAAqB;AACrB,+DAA+D;AAC/D,eAAe;AACf,sEAAsE;AACtE,gBAAgB;AAChB,wEAAwE;AACxE,SAAS;AAET,iEAAiE;AACjE,aAAa,EACb,gBAAgB;AAChB,6CAA6C;AAC7C,mBAAmB;AACnB,qEAAqE;AACrE,eAAe;AACf,6DAA6D;AAC7D,mBAAmB;AACnB,gFAAgF;AAChF,eAAe;AACf,+EAA+E;AAC/E,cAAc;AACd,mEAAmE;AACnE,QAAQ,EACR,mBAAmB;AAOnB,qDAAqD;AACrD,SAAS;AACT,qDAAqD;AACrD,QAAQ;AACR,0EAA0E;AAC1E,iBAAiB;AACjB,0EAA0E;AAC1E,gBAAgB;AAMhB,+EAA+E;AAC/E,sBAAsB,EACtB,kBAAkB;AAGlB,4EAA4E;AAC5E,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB;AACxB,6EAA6E;AAC7E,8BAA8B;AAE9B,kFAAkF;AAClF,eAAe;AAEf,yFAAyF;AACzF,iBAAiB;AAMjB,6EAA6E;AAC7E,aAAa;AAIb,8EAA8E;AAC9E,aAAa,EAEb,iBAAiB;AAEjB,6EAA6E;AAC7E,YAAY;AAEZ,qFAAqF;AACrF,iBAAiB;AAEjB,uFAAuF;AACvF,aAAa;AACb,6EAA6E;AAC7E,WAAW;AACX,0EAA0E;AAC1E,WAAW;AACX,+CAA+C;AAC/C,MAAM,EACN,WAAW,EACX,UAAU;AACV,kDAAkD;AAClD,UAAU;AACV,yDAAyD;AACzD,WAAW;AACX,8CAA8C;AAC9C,YAAY;AACZ,yDAAyD;AACzD,wBAAwB;AACxB,wDAAwD;AACxD,uBAAuB;AAKvB,2CAA2C;AAC3C,uBAAuB;AACvB,gEAAgE;AAChE,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB;AAEjB,2GAA2G;AAC3G,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB;AACnB,kFAAkF;AAClF,oBAAoB;AACpB,uGAAuG;AACvG,SAAS;AACT,0EAA0E;AAC1E,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,EAGnB,aAAa,EA0Cb,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,EACV,eAAe,EACf,2BAA2B,EAC3B,qBAAqB,EACrB,sBAAsB,EACtB,6BAA6B,EAC7B,uBAAuB,EACvB,wBAAwB,EACxB,yBAAyB,EACzB,mBAAmB,EACnB,oBAAoB,EACpB,yBAAyB,EACzB,qBAAqB,EACrB,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB,GAEzB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAAE,kBAAkB,EAA4B,MAAM,2BAA2B,CAAC;AAEzF,OAAO;AACL,yEAAyE;AACzE,iBAAiB;AACjB,0FAA0F;AAC1F,WAAW;AAUX,wEAAwE;AACxE,qBAAqB;AACrB,yEAAyE;AACzE,sBAAsB;AACtB,0EAA0E;AAC1E,oBAAoB,EACpB,qBAAqB;AACrB,iFAAiF;AACjF,mBAAmB,EACnB,oBAAoB;AACpB,6GAA6G;AAC7G,gBAAgB;AAChB,mFAAmF;AACnF,QAAQ;AACR,sFAAsF;AACtF,yBAAyB,GAC1B,MAAM,wBAAwB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO;AACL,0FAA0F;AAC1F,gBAAgB;AAEhB,4CAA4C;AAC5C,qBAAqB;AACrB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,gEAAgE;AAChE,qBAAqB;AACrB,gEAAgE;AAChE,qBAAqB,GACtB,MAAM,mBAAmB,CAAC;AA6B3B,OAAO;AACL,uFAAuF;AACvF,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,aAAa,EACb,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EACL,UAAU,EACV,WAAW,EACX,QAAQ,EACR,QAAQ,EACR,WAAW,EACX,OAAO,EACP,QAAQ,EACR,4BAA4B,EAC5B,qCAAqC,EACrC,uCAAuC,EACvC,UAAU,EACV,iBAAiB,EACjB,6BAA6B,EAC7B,oBAAoB,EACpB,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,iBAAiB,EACjB,gBAAgB,GACjB,MAAM,yBAAyB,CAAC;AAEjC,OAAO;AAEL,6EAA6E;AAC7E,oBAAoB;AAEpB,oDAAoD;AACpD,0BAA0B;AAC1B,mFAAmF;AACnF,iBAAiB,EACjB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC;AAOjC,wFAAwF;AACxF,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB;AAInB,iEAAiE;AACjE,0BAA0B;AAC1B,oEAAoE;AACpE,oBAAoB;AACpB,oFAAoF;AACpF,uBAAuB;AACvB,kHAAkH;AAClH,qBAAqB;AACrB,+DAA+D;AAC/D,eAAe;AACf,sEAAsE;AACtE,gBAAgB;AAChB,wEAAwE;AACxE,SAAS;AAET,iEAAiE;AACjE,aAAa,EACb,gBAAgB;AAChB,6CAA6C;AAC7C,mBAAmB;AACnB,qEAAqE;AACrE,eAAe;AACf,6DAA6D;AAC7D,mBAAmB;AACnB,gFAAgF;AAChF,eAAe;AACf,+EAA+E;AAC/E,cAAc;AACd,mEAAmE;AACnE,QAAQ,EACR,mBAAmB;AAOnB,qDAAqD;AACrD,SAAS;AACT,qDAAqD;AACrD,QAAQ;AACR,0EAA0E;AAC1E,iBAAiB;AACjB,0EAA0E;AAC1E,gBAAgB;AAMhB,+EAA+E;AAC/E,sBAAsB,EACtB,kBAAkB;AAGlB,4EAA4E;AAC5E,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB;AACxB,6EAA6E;AAC7E,8BAA8B;AAE9B,kFAAkF;AAClF,eAAe;AAEf,yFAAyF;AACzF,iBAAiB;AAMjB,6EAA6E;AAC7E,aAAa;AAIb,8EAA8E;AAC9E,aAAa,EAEb,iBAAiB,EAIjB,iBAAiB;AACjB,0DAA0D;AAC1D,iBAAiB;AAEjB,sFAAsF;AACtF,cAAc;AASd,sEAAsE;AACtE,UAAU,EACV,UAAU,EACV,YAAY,EACZ,gBAAgB,EAChB,YAAY,EACZ,oBAAoB;AAEpB,6EAA6E;AAC7E,YAAY;AAEZ,qFAAqF;AACrF,iBAAiB;AAEjB,uFAAuF;AACvF,aAAa;AACb,6EAA6E;AAC7E,WAAW;AACX,0EAA0E;AAC1E,WAAW;AACX,+CAA+C;AAC/C,MAAM,EACN,WAAW,EACX,UAAU;AACV,kDAAkD;AAClD,UAAU;AACV,yDAAyD;AACzD,WAAW;AACX,8CAA8C;AAC9C,YAAY;AACZ,yDAAyD;AACzD,wBAAwB;AACxB,wDAAwD;AACxD,uBAAuB;AAKvB,2CAA2C;AAC3C,uBAAuB;AACvB,gEAAgE;AAChE,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB;AAEjB,2GAA2G;AAC3G,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB;AACnB,kFAAkF;AAClF,oBAAoB;AACpB,uGAAuG;AACvG,SAAS;AACT,0EAA0E;AAC1E,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,EAGnB,aAAa,EA0Cb,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,EACV,eAAe,EACf,2BAA2B,EAC3B,qBAAqB,EACrB,sBAAsB,EACtB,6BAA6B,EAC7B,uBAAuB,EACvB,wBAAwB,EACxB,yBAAyB,EACzB,mBAAmB,EACnB,oBAAoB,EACpB,yBAAyB,EACzB,qBAAqB,EACrB,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB,GAEzB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAAE,kBAAkB,EAA4B,MAAM,2BAA2B,CAAC;AAEzF,OAAO;AACL,yEAAyE;AACzE,iBAAiB;AACjB,0FAA0F;AAC1F,WAAW;AAUX,wEAAwE;AACxE,qBAAqB;AACrB,yEAAyE;AACzE,sBAAsB;AACtB,0EAA0E;AAC1E,oBAAoB,EACpB,qBAAqB;AACrB,iFAAiF;AACjF,mBAAmB,EACnB,oBAAoB;AACpB,6GAA6G;AAC7G,gBAAgB;AAChB,mFAAmF;AACnF,QAAQ;AACR,sFAAsF;AACtF,yBAAyB,GAC1B,MAAM,wBAAwB,CAAC"}

package/dist/schema/parsed-tool.d.ts

@@ -1,4 +1,5 @@
 import * as S from "effect/Schema";
+import * as JSONSchema from "effect/JSONSchema";
 import type { ToolParameterModel } from "./bundle-types.js";
 /** Tool help content with format (rst, markdown, etc.) and rendered content. */
 export declare const HelpContent: S.Struct<{
@@ -15,6 +16,252 @@ export declare const Citation: S.Struct<{
     type: typeof S.String;
     content: typeof S.String;
 }>;
+export declare const DiscoverVia: S.Literal<["pattern", "tool_provided_metadata"]>;
+export declare const SortKey: S.Literal<["filename", "name", "designation", "dbkey"]>;
+export declare const SortComp: S.Literal<["lexical", "numeric"]>;
+export declare const ToolProvidedMetadataDatasetCollection: S.Struct<{
+    discover_via: S.Literal<["tool_provided_metadata"]>;
+    format: S.NullOr<typeof S.String>;
+    visible: typeof S.Boolean;
+    assign_primary_output: typeof S.Boolean;
+    directory: S.NullOr<typeof S.String>;
+    recurse: typeof S.Boolean;
+    match_relative_path: typeof S.Boolean;
+}>;
+export declare const FilePatternDatasetCollectionDescription: S.Struct<{
+    discover_via: S.Literal<["pattern"]>;
+    sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+    sort_comp: S.Literal<["lexical", "numeric"]>;
+    sort_reverse: typeof S.Boolean;
+    pattern: typeof S.String;
+    format: S.NullOr<typeof S.String>;
+    visible: typeof S.Boolean;
+    assign_primary_output: typeof S.Boolean;
+    directory: S.NullOr<typeof S.String>;
+    recurse: typeof S.Boolean;
+    match_relative_path: typeof S.Boolean;
+}>;
+export declare const DatasetCollectionDescription: S.Union<[S.Struct<{
+    discover_via: S.Literal<["pattern"]>;
+    sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+    sort_comp: S.Literal<["lexical", "numeric"]>;
+    sort_reverse: typeof S.Boolean;
+    pattern: typeof S.String;
+    format: S.NullOr<typeof S.String>;
+    visible: typeof S.Boolean;
+    assign_primary_output: typeof S.Boolean;
+    directory: S.NullOr<typeof S.String>;
+    recurse: typeof S.Boolean;
+    match_relative_path: typeof S.Boolean;
+}>, S.Struct<{
+    discover_via: S.Literal<["tool_provided_metadata"]>;
+    format: S.NullOr<typeof S.String>;
+    visible: typeof S.Boolean;
+    assign_primary_output: typeof S.Boolean;
+    directory: S.NullOr<typeof S.String>;
+    recurse: typeof S.Boolean;
+    match_relative_path: typeof S.Boolean;
+}>]>;
+export declare const ToolOutputDataset: S.Struct<{
+    type: S.Literal<["data"]>;
+    format: typeof S.String;
+    format_source: S.NullOr<typeof S.String>;
+    metadata_source: S.NullOr<typeof S.String>;
+    discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+        discover_via: S.Literal<["pattern"]>;
+        sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+        sort_comp: S.Literal<["lexical", "numeric"]>;
+        sort_reverse: typeof S.Boolean;
+        pattern: typeof S.String;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>, S.Struct<{
+        discover_via: S.Literal<["tool_provided_metadata"]>;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>]>>>;
+    from_work_dir: S.NullOr<typeof S.String>;
+    precreate_directory: typeof S.Boolean;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutputCollectionStructure: S.Struct<{
+    collection_type: S.NullOr<typeof S.String>;
+    collection_type_source: S.NullOr<typeof S.String>;
+    collection_type_from_rules: S.NullOr<typeof S.String>;
+    structured_like: S.NullOr<typeof S.String>;
+    discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+        discover_via: S.Literal<["pattern"]>;
+        sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+        sort_comp: S.Literal<["lexical", "numeric"]>;
+        sort_reverse: typeof S.Boolean;
+        pattern: typeof S.String;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>, S.Struct<{
+        discover_via: S.Literal<["tool_provided_metadata"]>;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>]>>>;
+}>;
+export declare const ToolOutputCollection: S.Struct<{
+    type: S.Literal<["collection"]>;
+    structure: S.Struct<{
+        collection_type: S.NullOr<typeof S.String>;
+        collection_type_source: S.NullOr<typeof S.String>;
+        collection_type_from_rules: S.NullOr<typeof S.String>;
+        structured_like: S.NullOr<typeof S.String>;
+        discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+            discover_via: S.Literal<["pattern"]>;
+            sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+            sort_comp: S.Literal<["lexical", "numeric"]>;
+            sort_reverse: typeof S.Boolean;
+            pattern: typeof S.String;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>, S.Struct<{
+            discover_via: S.Literal<["tool_provided_metadata"]>;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>]>>>;
+    }>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutputText: S.Struct<{
+    type: S.Literal<["text"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutputInteger: S.Struct<{
+    type: S.Literal<["integer"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutputFloat: S.Struct<{
+    type: S.Literal<["float"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutputBoolean: S.Struct<{
+    type: S.Literal<["boolean"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>;
+export declare const ToolOutput: S.Union<[S.Struct<{
+    type: S.Literal<["data"]>;
+    format: typeof S.String;
+    format_source: S.NullOr<typeof S.String>;
+    metadata_source: S.NullOr<typeof S.String>;
+    discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+        discover_via: S.Literal<["pattern"]>;
+        sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+        sort_comp: S.Literal<["lexical", "numeric"]>;
+        sort_reverse: typeof S.Boolean;
+        pattern: typeof S.String;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>, S.Struct<{
+        discover_via: S.Literal<["tool_provided_metadata"]>;
+        format: S.NullOr<typeof S.String>;
+        visible: typeof S.Boolean;
+        assign_primary_output: typeof S.Boolean;
+        directory: S.NullOr<typeof S.String>;
+        recurse: typeof S.Boolean;
+        match_relative_path: typeof S.Boolean;
+    }>]>>>;
+    from_work_dir: S.NullOr<typeof S.String>;
+    precreate_directory: typeof S.Boolean;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>, S.Struct<{
+    type: S.Literal<["collection"]>;
+    structure: S.Struct<{
+        collection_type: S.NullOr<typeof S.String>;
+        collection_type_source: S.NullOr<typeof S.String>;
+        collection_type_from_rules: S.NullOr<typeof S.String>;
+        structured_like: S.NullOr<typeof S.String>;
+        discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+            discover_via: S.Literal<["pattern"]>;
+            sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+            sort_comp: S.Literal<["lexical", "numeric"]>;
+            sort_reverse: typeof S.Boolean;
+            pattern: typeof S.String;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>, S.Struct<{
+            discover_via: S.Literal<["tool_provided_metadata"]>;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>]>>>;
+    }>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>, S.Struct<{
+    type: S.Literal<["text"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>, S.Struct<{
+    type: S.Literal<["integer"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>, S.Struct<{
+    type: S.Literal<["float"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>, S.Struct<{
+    type: S.Literal<["boolean"]>;
+    name: typeof S.String;
+    label: S.NullOr<typeof S.String>;
+    hidden: typeof S.Boolean;
+}>]>;
 /**
  * Effect Schema for parsed Galaxy tool metadata as returned by the ToolShed TRS API
  * or Galaxy's /api/tools/:id/parsed endpoint.
@@ -25,7 +272,90 @@ export declare const ParsedTool: S.Struct<{
     name: typeof S.String;
     description: S.transform<S.NullOr<typeof S.String>, S.NullOr<typeof S.String>>;
     inputs: S.Array$<S.Schema<ToolParameterModel, ToolParameterModel, never>>;
-    outputs: S.Array$<typeof S.Unknown>;
+    outputs: S.Array$<S.Union<[S.Struct<{
+        type: S.Literal<["data"]>;
+        format: typeof S.String;
+        format_source: S.NullOr<typeof S.String>;
+        metadata_source: S.NullOr<typeof S.String>;
+        discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+            discover_via: S.Literal<["pattern"]>;
+            sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+            sort_comp: S.Literal<["lexical", "numeric"]>;
+            sort_reverse: typeof S.Boolean;
+            pattern: typeof S.String;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>, S.Struct<{
+            discover_via: S.Literal<["tool_provided_metadata"]>;
+            format: S.NullOr<typeof S.String>;
+            visible: typeof S.Boolean;
+            assign_primary_output: typeof S.Boolean;
+            directory: S.NullOr<typeof S.String>;
+            recurse: typeof S.Boolean;
+            match_relative_path: typeof S.Boolean;
+        }>]>>>;
+        from_work_dir: S.NullOr<typeof S.String>;
+        precreate_directory: typeof S.Boolean;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>, S.Struct<{
+        type: S.Literal<["collection"]>;
+        structure: S.Struct<{
+            collection_type: S.NullOr<typeof S.String>;
+            collection_type_source: S.NullOr<typeof S.String>;
+            collection_type_from_rules: S.NullOr<typeof S.String>;
+            structured_like: S.NullOr<typeof S.String>;
+            discover_datasets: S.NullOr<S.Array$<S.Union<[S.Struct<{
+                discover_via: S.Literal<["pattern"]>;
+                sort_key: S.Literal<["filename", "name", "designation", "dbkey"]>;
+                sort_comp: S.Literal<["lexical", "numeric"]>;
+                sort_reverse: typeof S.Boolean;
+                pattern: typeof S.String;
+                format: S.NullOr<typeof S.String>;
+                visible: typeof S.Boolean;
+                assign_primary_output: typeof S.Boolean;
+                directory: S.NullOr<typeof S.String>;
+                recurse: typeof S.Boolean;
+                match_relative_path: typeof S.Boolean;
+            }>, S.Struct<{
+                discover_via: S.Literal<["tool_provided_metadata"]>;
+                format: S.NullOr<typeof S.String>;
+                visible: typeof S.Boolean;
+                assign_primary_output: typeof S.Boolean;
+                directory: S.NullOr<typeof S.String>;
+                recurse: typeof S.Boolean;
+                match_relative_path: typeof S.Boolean;
+            }>]>>>;
+        }>;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>, S.Struct<{
+        type: S.Literal<["text"]>;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>, S.Struct<{
+        type: S.Literal<["integer"]>;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>, S.Struct<{
+        type: S.Literal<["float"]>;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>, S.Struct<{
+        type: S.Literal<["boolean"]>;
+        name: typeof S.String;
+        label: S.NullOr<typeof S.String>;
+        hidden: typeof S.Boolean;
+    }>]>>;
     citations: S.Array$<S.Struct<{
         type: typeof S.String;
         content: typeof S.String;
@@ -43,5 +373,20 @@ export declare const ParsedTool: S.Struct<{
         content: typeof S.String;
     }>, typeof S.Null]>>;
 }>;
+export declare const parsedToolSchema: JSONSchema.JsonSchema7Root;
+export type DiscoverVia = S.Schema.Type<typeof DiscoverVia>;
+export type SortKey = S.Schema.Type<typeof SortKey>;
+export type SortComp = S.Schema.Type<typeof SortComp>;
+export type ToolProvidedMetadataDatasetCollection = S.Schema.Type<typeof ToolProvidedMetadataDatasetCollection>;
+export type FilePatternDatasetCollectionDescription = S.Schema.Type<typeof FilePatternDatasetCollectionDescription>;
+export type DatasetCollectionDescription = S.Schema.Type<typeof DatasetCollectionDescription>;
+export type ToolOutputDataset = S.Schema.Type<typeof ToolOutputDataset>;
+export type ToolOutputCollectionStructure = S.Schema.Type<typeof ToolOutputCollectionStructure>;
+export type ToolOutputCollection = S.Schema.Type<typeof ToolOutputCollection>;
+export type ToolOutputText = S.Schema.Type<typeof ToolOutputText>;
+export type ToolOutputInteger = S.Schema.Type<typeof ToolOutputInteger>;
+export type ToolOutputFloat = S.Schema.Type<typeof ToolOutputFloat>;
+export type ToolOutputBoolean = S.Schema.Type<typeof ToolOutputBoolean>;
+export type ToolOutput = S.Schema.Type<typeof ToolOutput>;
 export type ParsedTool = S.Schema.Type<typeof ParsedTool>;
 //# sourceMappingURL=parsed-tool.d.ts.map

package/dist/schema/parsed-tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"parsed-tool.d.ts","sourceRoot":"","sources":["../../src/schema/parsed-tool.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AACnC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAEhD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAE5D,gFAAgF;AAChF,eAAO,MAAM,WAAW;;;EAGtB,CAAC;AAEH,oEAAoE;AACpE,eAAO,MAAM,QAAQ;;;EAGnB,CAAC;AAEH,+CAA+C;AAC/C,eAAO,MAAM,QAAQ;;;EAGnB,CAAC;AAEH,eAAO,MAAM,WAAW,kDAAiD,CAAC;AAC1E,eAAO,MAAM,OAAO,yDAAwD,CAAC;AAC7E,eAAO,MAAM,QAAQ,mCAAkC,CAAC;AAYxD,eAAO,MAAM,qCAAqC;;;;;;;;EAGhD,CAAC;AAEH,eAAO,MAAM,uCAAuC;;;;;;;;;;;;EAOlD,CAAC;AAEH,eAAO,MAAM,4BAA4B;;;;;;;;;;;;;;;;;;;;IAGxC,CAAC;AAQF,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAS5B,CAAC;AAEH,eAAO,MAAM,6BAA6B;;;;;;;;;;;;;;;;;;;;;;;;;;EAMxC,CAAC;AAEH,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAI/B,CAAC;AAEH,eAAO,MAAM,cAAc;;;;;EAGzB,CAAC;AAEH,eAAO,MAAM,iBAAiB;;;;;EAG5B,CAAC;AAEH,eAAO,MAAM,eAAe;;;;;EAG1B,CAAC;AAEH,eAAO,MAAM,iBAAiB;;;;;EAG5B,CAAC;AAEH,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;IAOtB,CAAC;AAoBF;;;GAGG;AACH,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAcrB,CAAC;AAEH,eAAO,MAAM,gBAAgB,4BAA+D,CAAC;AAE7F,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,WAAW,CAAC,CAAC;AAC5D,MAAM,MAAM,OAAO,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,OAAO,CAAC,CAAC;AACpD,MAAM,MAAM,QAAQ,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,QAAQ,CAAC,CAAC;AACtD,MAAM,MAAM,qCAAqC,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAC/D,OAAO,qCAAqC,CAC7C,CAAC;AACF,MAAM,MAAM,uCAAuC,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CACjE,OAAO,uCAAuC,CAC/C,CAAC;AACF,MAAM,MAAM,4BAA4B,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,4BAA4B,CAAC,CAAC;AAC9F,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,iBAAiB,CAAC,CAAC;AACxE,MAAM,MAAM,6BAA6B,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,6BAA6B,CAAC,CAAC;AAChG,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAC9E,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,cAAc,CAAC,CAAC;AAClE,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,iBAAiB,CAAC,CAAC;AACxE,MAAM,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,eAAe,CAAC,CAAC;AACpE,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,iBAAiB,CAAC,CAAC;AACxE,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,UAAU,CAAC,CAAC;AAC1D,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,UAAU,CAAC,CAAC"}

package/dist/schema/parsed-tool.js

@@ -1,4 +1,5 @@
 import * as S from "effect/Schema";
+import * as JSONSchema from "effect/JSONSchema";
 /** Tool help content with format (rst, markdown, etc.) and rendered content. */
 export const HelpContent = S.Struct({
     format: S.String,
@@ -14,6 +15,75 @@ export const Citation = S.Struct({
     type: S.String,
     content: S.String,
 });
+export const DiscoverVia = S.Literal("pattern", "tool_provided_metadata");
+export const SortKey = S.Literal("filename", "name", "designation", "dbkey");
+export const SortComp = S.Literal("lexical", "numeric");
+const DatasetCollectionDescriptionBase = S.Struct({
+    discover_via: DiscoverVia,
+    format: S.NullOr(S.String),
+    visible: S.Boolean,
+    assign_primary_output: S.Boolean,
+    directory: S.NullOr(S.String),
+    recurse: S.Boolean,
+    match_relative_path: S.Boolean,
+});
+export const ToolProvidedMetadataDatasetCollection = S.Struct({
+    ...DatasetCollectionDescriptionBase.fields,
+    discover_via: S.Literal("tool_provided_metadata"),
+});
+export const FilePatternDatasetCollectionDescription = S.Struct({
+    ...DatasetCollectionDescriptionBase.fields,
+    discover_via: S.Literal("pattern"),
+    sort_key: SortKey,
+    sort_comp: SortComp,
+    sort_reverse: S.Boolean,
+    pattern: S.String,
+});
+export const DatasetCollectionDescription = S.Union(FilePatternDatasetCollectionDescription, ToolProvidedMetadataDatasetCollection);
+const ToolOutputBase = S.Struct({
+    name: S.String,
+    label: S.NullOr(S.String),
+    hidden: S.Boolean,
+});
+export const ToolOutputDataset = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("data"),
+    format: S.String,
+    format_source: S.NullOr(S.String),
+    metadata_source: S.NullOr(S.String),
+    discover_datasets: S.NullOr(S.Array(DatasetCollectionDescription)),
+    from_work_dir: S.NullOr(S.String),
+    precreate_directory: S.Boolean,
+});
+export const ToolOutputCollectionStructure = S.Struct({
+    collection_type: S.NullOr(S.String),
+    collection_type_source: S.NullOr(S.String),
+    collection_type_from_rules: S.NullOr(S.String),
+    structured_like: S.NullOr(S.String),
+    discover_datasets: S.NullOr(S.Array(DatasetCollectionDescription)),
+});
+export const ToolOutputCollection = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("collection"),
+    structure: ToolOutputCollectionStructure,
+});
+export const ToolOutputText = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("text"),
+});
+export const ToolOutputInteger = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("integer"),
+});
+export const ToolOutputFloat = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("float"),
+});
+export const ToolOutputBoolean = S.Struct({
+    ...ToolOutputBase.fields,
+    type: S.Literal("boolean"),
+});
+export const ToolOutput = S.Union(ToolOutputDataset, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean);
 /** Normalize empty string to null for description field. */
 const NullableDescription = S.transform(S.NullOr(S.String), S.NullOr(S.String), {
     decode: (val) => (val === "" ? null : val),
@@ -26,7 +96,7 @@ const NullableDescription = S.transform(S.NullOr(S.String), S.NullOr(S.String),
  * object-shaped guard here and supply the TS type via the generic parameter.
  * `ParsedTool` payloads come from Python's `model_dump()` — already trusted.
  */
-const ToolParameterModelSchema = S.declare((input) => typeof input === "object" && input !== null && !Array.isArray(input));
+const ToolParameterModelSchema = S.declare((input) => typeof input === "object" && input !== null && !Array.isArray(input)).annotations({ jsonSchema: { type: "object" } });
 /**
  * Effect Schema for parsed Galaxy tool metadata as returned by the ToolShed TRS API
  * or Galaxy's /api/tools/:id/parsed endpoint.
@@ -37,7 +107,7 @@ export const ParsedTool = S.Struct({
     name: S.String,
     description: NullableDescription,
     inputs: S.Array(ToolParameterModelSchema),
-    outputs: S.Array(S.Unknown),
+    outputs: S.Array(ToolOutput),
     citations: S.Array(Citation),
     license: S.NullOr(S.String),
     profile: S.NullOr(S.String),
@@ -46,4 +116,5 @@ export const ParsedTool = S.Struct({
     xrefs: S.Array(XrefDict),
     help: S.optional(S.Union(HelpContent, S.Null)),
 });
+export const parsedToolSchema = JSONSchema.make(ParsedTool, { target: "jsonSchema2020-12" });
 //# sourceMappingURL=parsed-tool.js.map

package/dist/schema/parsed-tool.js.map

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