@galaxy-tool-util/schema 1.1.0 → 1.5.0

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, 
@@ -99,8 +99,32 @@ 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, 
+/** Draft workflow sentinel pattern (mirrors gxformat2/draft.py). */
+TODO_SENTINEL_PATTERN, PLAN_FIELDS, DRAFT_CLASS, isTodoSentinel, 
+/** True iff doc carries `class: GalaxyWorkflowDraft`. */
+isDraftWorkflow, 
+/** Walk a draft workflow once; collect every TODO sentinel + `_plan_*` field. */
+detectDraft, 
+/** Validate a draft workflow: structural decode + topology + sentinel-form + warnings. Does not throw. */
+validateDraft, 
+/** Topologically-ordered "what to work on next" for a draft workflow; prompt-shaped work[]. */
+nextDraftStep, type NextStepResult, 
+/** Trim a draft workflow to its concrete subset; cascade drops + multi-source rewrites. */
+extractConcreteSubset, type DropReason, type DroppedStep, type DroppedOutput, type RewrittenStepInput, type ExtractResult, 
+/** Strip `_plan_*` planning fields from every step + workflow root (recursive over draft subworkflows). */
+stripPlanFields, type StrippedPlanField, type StripPlanFieldsResult, 
+/** Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any (sub)workflow now fully concrete. */
+promoteFullyConcreteDrafts, type PromoteFullyConcreteDraftsResult, type PlanField, type StepPath, type TodoLocation, type TodoHit, type PlanHit, type DraftSurvey, type DraftValidationDiagnostic, type DraftValidationResult, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */
 serializeWorkflow, type SerializeWorkflowOptions, 
 /** Resolve workflow format from an optional override, falling back to detectFormat. */
@@ -132,7 +156,7 @@ checkStrictStructure,
 /** Inject `class` discriminator into workflow dict when missing (recursive over step subworkflows). */
 withClass, 
 /** Effect-schema validator dispatch mirroring gxformat2/validators.py. */
-validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, type StepStatus, SKIP_STATUSES, type ValidationStepResult, type CleanStepResult, type ResolvedOutputType, type ConnectionResult, type ConnectionStepResult, type ConnectionValidationReport, type WorkflowEntry, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type DiffType, type DiffSeverity, type BenignArtifact, type StepDiff, type SkipWorkflowReason, type FailureClass, type StepResult, type RoundTripResult, type StepIdMappingResult, type RoundTripValidationResult, type SingleRoundTripReport, type SingleExportReport, type StepEncodeStatus, type ToNativeResult, type WorkflowSourceFormat, type ExportResult, type ConvertResult, type WorkflowValidationResult, type LintWorkflowResult, type WorkflowCleanResult, type CategoryGroup, type TreeValidationReport, type LintTreeReport, type TreeCleanReport, type WorkflowExportResult, type ExportTreeReport, type WorkflowToNativeResult, type ToNativeTreeReport, type ToolFailureMode, type RoundTripTreeReport, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, type CleanWorkflowOptions, } from "./workflow/index.js";
+validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, type StepStatus, SKIP_STATUSES, type ValidationStepResult, type CleanStepResult, type ResolvedOutputType, type ConnectionResult, type ConnectionStepResult, type ConnectionValidationReport, type WorkflowEntry, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type DraftValidationDiagnosticReport, type DraftSurveyReport, type SingleDraftValidationReport, type DraftExtractDropReport, type DraftExtractRewriteReport, type SingleDraftExtractReport, type DiffType, type DiffSeverity, type BenignArtifact, type StepDiff, type SkipWorkflowReason, type FailureClass, type StepResult, type RoundTripResult, type StepIdMappingResult, type RoundTripValidationResult, type SingleRoundTripReport, type SingleExportReport, type StepEncodeStatus, type ToNativeResult, type WorkflowSourceFormat, type ExportResult, type ConvertResult, type WorkflowValidationResult, type LintWorkflowResult, type WorkflowCleanResult, type CategoryGroup, type TreeValidationReport, type LintTreeReport, type TreeCleanReport, type WorkflowExportResult, type ExportTreeReport, type WorkflowToNativeResult, type ToNativeTreeReport, type ToolFailureMode, type RoundTripTreeReport, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, type CleanWorkflowOptions, } from "./workflow/index.js";
 export { ToolStateValidator, type ToolStateDiagnostic } from "./tool-state-validator.js";
 export { 
 /** Validate a parsed *.gxwf-tests.yml / Planemo *-tests.yml document. */
@@ -161,4 +185,14 @@ isCompatibleType,
 jsTypeOf, 
 /** Cross-check a tests doc against workflow shape; emits JSON-pointer diagnostics. */
 checkTestsAgainstWorkflow, } from "./test-format/index.js";
+export { 
+/** Validate a parsed user-defined Galaxy tool source document. */
+validateUserToolSource, 
+/** Raw JSON Schema synced from galaxy.tool_util_models.DynamicToolSources. */
+userToolSourceSchema, 
+/** Run only the semantic (model_validator) checks — internal helper, exposed for tests. */
+runSemanticChecks, type UserToolSourceDiagnostic, type ValidateUserToolSourceOptions, } from "./user-tool-source/index.js";
+export { 
+/** Parse an inline GalaxyUserTool `tool_representation` dict into a ParsedTool. */
+parseInlineTool, type InlineRepresentation, } from "./user-tool-parse/index.js";
 //# sourceMappingURL=index.d.ts.map

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, 
@@ -83,9 +83,31 @@ 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, 
+/** Draft workflow sentinel pattern (mirrors gxformat2/draft.py). */
+TODO_SENTINEL_PATTERN, PLAN_FIELDS, DRAFT_CLASS, isTodoSentinel, 
+/** True iff doc carries `class: GalaxyWorkflowDraft`. */
+isDraftWorkflow, 
+/** Walk a draft workflow once; collect every TODO sentinel + `_plan_*` field. */
+detectDraft, 
+/** Validate a draft workflow: structural decode + topology + sentinel-form + warnings. Does not throw. */
+validateDraft, 
+/** Topologically-ordered "what to work on next" for a draft workflow; prompt-shaped work[]. */
+nextDraftStep, 
+/** Trim a draft workflow to its concrete subset; cascade drops + multi-source rewrites. */
+extractConcreteSubset, 
+/** Strip `_plan_*` planning fields from every step + workflow root (recursive over draft subworkflows). */
+stripPlanFields, 
+/** Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any (sub)workflow now fully concrete. */
+promoteFullyConcreteDrafts, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */
 serializeWorkflow, 
 /** Resolve workflow format from an optional override, falling back to detectFormat. */
@@ -117,7 +139,7 @@ checkStrictStructure,
 /** Inject `class` discriminator into workflow dict when missing (recursive over step subworkflows). */
 withClass, 
 /** Effect-schema validator dispatch mirroring gxformat2/validators.py. */
-validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, SKIP_STATUSES, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./workflow/index.js";
+validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, SKIP_STATUSES, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./workflow/index.js";
 export { ToolStateValidator } from "./tool-state-validator.js";
 export { 
 /** Validate a parsed *.gxwf-tests.yml / Planemo *-tests.yml document. */
@@ -138,4 +160,14 @@ isCompatibleType,
 jsTypeOf, 
 /** Cross-check a tests doc against workflow shape; emits JSON-pointer diagnostics. */
 checkTestsAgainstWorkflow, } from "./test-format/index.js";
+export { 
+/** Validate a parsed user-defined Galaxy tool source document. */
+validateUserToolSource, 
+/** Raw JSON Schema synced from galaxy.tool_util_models.DynamicToolSources. */
+userToolSourceSchema, 
+/** Run only the semantic (model_validator) checks — internal helper, exposed for tests. */
+runSemanticChecks, } from "./user-tool-source/index.js";
+export { 
+/** Parse an inline GalaxyUserTool `tool_representation` dict into a ParsedTool. */
+parseInlineTool, } from "./user-tool-parse/index.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"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,oEAAoE;AACpE,qBAAqB,EACrB,WAAW,EACX,WAAW,EACX,cAAc;AACd,yDAAyD;AACzD,eAAe;AACf,iFAAiF;AACjF,WAAW;AACX,0GAA0G;AAC1G,aAAa;AACb,+FAA+F;AAC/F,aAAa;AAEb,2FAA2F;AAC3F,qBAAqB;AAMrB,2GAA2G;AAC3G,eAAe;AAGf,2GAA2G;AAC3G,0BAA0B;AAU1B,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,EAgDb,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,EACV,eAAe,EACf,2BAA2B,EAC3B,qBAAqB,EACrB,sBAAsB,EACtB,gCAAgC,EAChC,6BAA6B,EAC7B,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;AAEhC,OAAO;AACL,kEAAkE;AAClE,sBAAsB;AACtB,8EAA8E;AAC9E,oBAAoB;AACpB,2FAA2F;AAC3F,iBAAiB,GAGlB,MAAM,6BAA6B,CAAC;AAErC,OAAO;AACL,mFAAmF;AACnF,eAAe,GAEhB,MAAM,4BAA4B,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 +373,23 @@ export declare const ParsedTool: S.Struct<{
         content: typeof S.String;
     }>, typeof S.Null]>>;
 }>;
+export declare const parsedToolSchema: JSONSchema.JsonSchema7Root;
+export type HelpContent = S.Schema.Type<typeof HelpContent>;
+export type XrefDict = S.Schema.Type<typeof XrefDict>;
+export type Citation = S.Schema.Type<typeof Citation>;
+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

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