@galaxy-tool-util/schema 1.7.2 → 1.8.2

package/dist/index.d.ts

@@ -52,7 +52,11 @@ DraftWorkflowStepSchema, type NativeGalaxyWorkflow,
 /** Schema for raw native (.ga) Galaxy workflows. */
 NativeGalaxyWorkflowSchema, 
 /** Normalize a raw format2 workflow — fills defaults, resolves implicit fields. */
-normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, 
+normalizedFormat2, 
+/** Expand a step's raw `in` shorthand into normalized {id, source} entries. */
+normalizeStepIn, 
+/** Expand a step's raw `out` shorthand into normalized {id} entries. */
+normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, 
 /** Normalize a raw native (.ga) workflow — fills defaults, resolves implicit fields. */
 normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, 
 /** Merge step connection info into tool_state for validation. */

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO;AACL,0FAA0F;AAC1F,gBAAgB,EAChB,KAAK,mBAAmB;AACxB,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;AAE3B,OAAO;AACL,2CAA2C;AAC3C,KAAK,wBAAwB;AAC7B,2EAA2E;AAC3E,KAAK,kBAAkB;AACvB,4DAA4D;AAC5D,KAAK,oBAAoB;AACzB,yEAAyE;AACzE,KAAK,uBAAuB;AAC5B,6DAA6D;AAC7D,KAAK,wBAAwB,EAC7B,KAAK,qBAAqB,EAC1B,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,oBAAoB,EACzB,KAAK,yBAAyB,EAC9B,KAAK,uBAAuB,EAC5B,KAAK,qBAAqB,EAC1B,KAAK,qBAAqB,EAC1B,KAAK,oBAAoB,EACzB,KAAK,yBAAyB;AAC9B,sDAAsD;AACtD,KAAK,eAAe;AACpB,iEAAiE;AACjE,KAAK,UAAU,GAChB,MAAM,0BAA0B,CAAC;AAElC,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,EACL,KAAK,cAAc;AACnB,6EAA6E;AAC7E,oBAAoB,EACpB,KAAK,mBAAmB;AACxB,2GAA2G;AAC3G,yBAAyB;AACzB,+HAA+H;AAC/H,6BAA6B,EAC7B,KAAK,iBAAiB;AACtB,mGAAmG;AACnG,uBAAuB,EACvB,KAAK,oBAAoB;AACzB,oDAAoD;AACpD,0BAA0B;AAC1B,mFAAmF;AACnF,iBAAiB;AACjB,+EAA+E;AAC/E,eAAe;AACf,wEAAwE;AACxE,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B;AAChC,wFAAwF;AACxF,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa;AAClB,iEAAiE;AACjE,0BAA0B;AAC1B,oEAAoE;AACpE,oBAAoB;AACpB,4EAA4E;AAC5E,8BAA8B;AAC9B,oFAAoF;AACpF,uBAAuB;AACvB,kHAAkH;AAClH,qBAAqB;AACrB,+DAA+D;AAC/D,eAAe;AACf,sEAAsE;AACtE,gBAAgB;AAChB,wEAAwE;AACxE,SAAS,EACT,KAAK,kBAAkB;AACvB,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,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB;AACrB,qDAAqD;AACrD,SAAS;AACT,qDAAqD;AACrD,QAAQ;AACR,0EAA0E;AAC1E,iBAAiB;AACjB,0EAA0E;AAC1E,gBAAgB,EAChB,KAAK,oBAAoB,EACzB,KAAK,0BAA0B,EAC/B,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB;AACvB,+EAA+E;AAC/E,sBAAsB,EACtB,kBAAkB,EAClB,KAAK,cAAc,EACnB,KAAK,kBAAkB;AACvB,4EAA4E;AAC5E,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB;AACxB,6EAA6E;AAC7E,8BAA8B,EAC9B,KAAK,eAAe;AACpB,kFAAkF;AAClF,eAAe,EACf,KAAK,qBAAqB;AAC1B,yFAAyF;AACzF,iBAAiB,EACjB,KAAK,eAAe,EACpB,KAAK,sBAAsB,EAC3B,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,qBAAqB;AAC1B,6EAA6E;AAC7E,aAAa,EACb,KAAK,4BAA4B,EACjC,KAAK,iBAAiB,EACtB,KAAK,wBAAwB;AAC7B,8EAA8E;AAC9E,aAAa,EACb,KAAK,mBAAmB,EACxB,iBAAiB,EACjB,KAAK,cAAc;AACnB,oGAAoG;AACpG,KAAK,cAAc,EACnB,iBAAiB;AACjB,0DAA0D;AAC1D,iBAAiB,EACjB,KAAK,gBAAgB;AACrB,sFAAsF;AACtF,cAAc,EACd,KAAK,aAAa,EAClB,KAAK,iBAAiB,EACtB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACxB,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAClB,KAAK,iBAAiB,EACtB,KAAK,iBAAiB;AACtB,sEAAsE;AACtE,UAAU,EACV,UAAU,EACV,YAAY,EACZ,gBAAgB,EAChB,YAAY,EACZ,oBAAoB,EACpB,KAAK,UAAU;AACf,6EAA6E;AAC7E,YAAY,EACZ,KAAK,cAAc;AACnB,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,EACb,KAAK,cAAc;AACnB,2FAA2F;AAC3F,qBAAqB,EACrB,KAAK,UAAU,EACf,KAAK,WAAW,EAChB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,aAAa;AAClB,2GAA2G;AAC3G,eAAe,EACf,KAAK,iBAAiB,EACtB,KAAK,qBAAqB;AAC1B,2GAA2G;AAC3G,0BAA0B,EAC1B,KAAK,gCAAgC,EACrC,KAAK,SAAS,EACd,KAAK,QAAQ,EACb,KAAK,YAAY,EACjB,KAAK,OAAO,EACZ,KAAK,OAAO,EACZ,KAAK,WAAW,EAChB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB;AAC1B,qFAAqF;AACrF,iBAAiB,EACjB,KAAK,wBAAwB;AAC7B,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,EACvB,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW;AAChB,2CAA2C;AAC3C,uBAAuB;AACvB,gEAAgE;AAChE,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB,EACjB,KAAK,WAAW;AAChB,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,EAEnB,KAAK,UAAU,EACf,aAAa,EACb,KAAK,oBAAoB,EACzB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,EACrB,KAAK,oBAAoB,EACzB,KAAK,0BAA0B,EAC/B,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,sBAAsB,EAC3B,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,+BAA+B,EACpC,KAAK,iBAAiB,EACtB,KAAK,2BAA2B,EAChC,KAAK,wBAAwB,EAC7B,KAAK,sBAAsB,EAC3B,KAAK,yBAAyB,EAC9B,KAAK,wBAAwB,EAC7B,KAAK,QAAQ,EACb,KAAK,YAAY,EACjB,KAAK,cAAc,EACnB,KAAK,QAAQ,EACb,KAAK,kBAAkB,EACvB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,eAAe,EACpB,KAAK,mBAAmB,EACxB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,E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package/dist/index.js

@@ -37,7 +37,11 @@ DraftWorkflowStepSchema,
 /** Schema for raw native (.ga) Galaxy workflows. */
 NativeGalaxyWorkflowSchema, 
 /** Normalize a raw format2 workflow — fills defaults, resolves implicit fields. */
-normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, 
+normalizedFormat2, 
+/** Expand a step's raw `in` shorthand into normalized {id, source} entries. */
+normalizeStepIn, 
+/** Expand a step's raw `out` shorthand into normalized {id} entries. */
+normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, 
 /** Normalize a raw native (.ga) workflow — fills defaults, resolves implicit fields. */
 normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, 
 /** Merge step connection info into tool_state for validation. */

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/workflow/index.d.ts

@@ -1,7 +1,7 @@
 export { serializeWorkflow, resolveFormat, type SerializeWorkflowOptions } from "./serialize.js";
 export { type GalaxyWorkflow, GalaxyWorkflowSchema, type GalaxyWorkflowDraft, GalaxyWorkflowDraftSchema, type DraftWorkflowStep, DraftWorkflowStepSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
-export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, type ToFormat2Options, type Format2StateOverride, toNative, type ToNativeOptions, toFormat2Stateful, toNativeStateful, type StepConversionStatus, type StepConversionFailureClass, type StatefulExportResult, type StatefulNativeResult, type ToolInputsResolver, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, type ToFormat2Options, type Format2StateOverride, toNative, type ToNativeOptions, toFormat2Stateful, toNativeStateful, type StepConversionStatus, type StepConversionFailureClass, type StatefulExportResult, type StatefulNativeResult, type ToolInputsResolver, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";

package/dist/workflow/index.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/index.js

@@ -5,7 +5,7 @@ export { GalaxyWorkflowSchema, GalaxyWorkflowDraftSchema, DraftWorkflowStepSchem
 // Plain JSON Schema siblings for downstream packagers (issue #108)
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
 // Normalized workflow types + normalizers
-export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";

package/dist/workflow/index.js.map

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package/dist/workflow/normalized/format2.d.ts

@@ -147,4 +147,30 @@ export declare const NormalizedFormat2StepSchema: Schema.Struct<{
 }>;
 export type NormalizedFormat2Step = typeof NormalizedFormat2StepSchema.Type;
 export declare function normalizedFormat2(raw: unknown): NormalizedFormat2Workflow;
+/**
+ * Expand a step's raw `in` value into normalized `{id, source, ...}` entries,
+ * covering every gxformat2 shorthand:
+ *   - list of strings:   in: [query]                 → {id: "query"}
+ *   - list of objects:   in: [{id: query, source}]   → {id: "query", source}
+ *   - map to string:     in: {query: step/out}        → {id: "query", source}
+ *   - map to list:       in: {query: [a, b]}          → {id: "query", source: [a, b]}
+ *   - map to object:     in: {query: {source, ...}}   → {id: "query", source, ...}
+ *
+ * Pure and value-based (no AST/position awareness) so callers that hold a raw
+ * step dict — e.g. an editor walking a parsed document — can reuse the same
+ * shorthand rules instead of re-deriving them. Note that connections declared
+ * via `{$link: ...}` inside `state` are resolved separately during full step
+ * normalization, not here.
+ */
+export declare function normalizeStepIn(raw: unknown): NormalizedFormat2StepInput[];
+/**
+ * Expand a step's raw `out` value into normalized `{id, ...}` entries, covering
+ * every gxformat2 shorthand:
+ *   - list of strings:   out: [out_file1]             → {id: "out_file1"}
+ *   - list of objects:   out: [{id: out_file1, ...}]  → {id: "out_file1", ...}
+ *   - map:               out: {out_file1: {...}}      → {id: "out_file1", ...}
+ *
+ * Pure and value-based — see {@link normalizeStepIn}.
+ */
+export declare function normalizeStepOut(raw: unknown): NormalizedFormat2StepOutput[];
 //# sourceMappingURL=format2.d.ts.map

package/dist/workflow/normalized/format2.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"format2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/format2.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAmBhC,eAAO,MAAM,gCAAgC;;;;;EAK3C,CAAC;AACH,MAAM,MAAM,0BAA0B,GAAG,OAAO,gCAAgC,CAAC,IAAI,CAAC;AAEtF,eAAO,MAAM,iCAAiC;;;;;;;;;EAW5C,CAAC;AACH,MAAM,MAAM,2BAA2B,GAAG,OAAO,iCAAiC,CAAC,IAAI,CAAC;AAExF,eAAO,MAAM,4BAA4B;;;;;;;;;;EAYvC,CAAC;AACH,MAAM,MAAM,sBAAsB,GAAG,OAAO,4BAA4B,CAAC,IAAI,CAAC;AAE9E,eAAO,MAAM,6BAA6B;;;;;;EAMxC,CAAC;AACH,MAAM,MAAM,uBAAuB,GAAG,OAAO,6BAA6B,CAAC,IAAI,CAAC;AAGhF,eAAO,MAAM,+BAA+B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAe1C,CAAC;AACH,MAAM,MAAM,yBAAyB,GAAG,OAAO,+BAA+B,CAAC,IAAI,CAAC;AAEpF,eAAO,MAAM,2BAA2B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6BtC,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAI5E,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,OAAO,GAAG,yBAAyB,CAsBzE;AAqKD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,OAAO,GAAG,0BAA0B,EAAE,CA2B1E;AAED;;;;;;;;GAQG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,OAAO,GAAG,2BAA2B,EAAE,CAoB5E"}

package/dist/workflow/normalized/format2.js

@@ -212,8 +212,8 @@ function _normalizeSteps(raw, subworkflows) {
     return result;
 }
 function _normalizeStep(raw, id, subworkflows) {
-    const stepIn = _normalizeStepIn(raw.in);
-    const stepOut = _normalizeStepOut(raw.out);
+    const stepIn = normalizeStepIn(raw.in);
+    const stepOut = normalizeStepOut(raw.out);
     const run = _resolveRun(raw.run, subworkflows);
     // Resolve $link references in state: replace with ConnectedValue and
     // collect corresponding in entries for downstream connection injection
@@ -253,7 +253,22 @@ function _normalizeStep(raw, id, subworkflows) {
         runtime_inputs: raw.runtime_inputs,
     };
 }
-function _normalizeStepIn(raw) {
+/**
+ * Expand a step's raw `in` value into normalized `{id, source, ...}` entries,
+ * covering every gxformat2 shorthand:
+ *   - list of strings:   in: [query]                 → {id: "query"}
+ *   - list of objects:   in: [{id: query, source}]   → {id: "query", source}
+ *   - map to string:     in: {query: step/out}        → {id: "query", source}
+ *   - map to list:       in: {query: [a, b]}          → {id: "query", source: [a, b]}
+ *   - map to object:     in: {query: {source, ...}}   → {id: "query", source, ...}
+ *
+ * Pure and value-based (no AST/position awareness) so callers that hold a raw
+ * step dict — e.g. an editor walking a parsed document — can reuse the same
+ * shorthand rules instead of re-deriving them. Note that connections declared
+ * via `{$link: ...}` inside `state` are resolved separately during full step
+ * normalization, not here.
+ */
+export function normalizeStepIn(raw) {
     if (!raw)
         return [];
     if (Array.isArray(raw)) {
@@ -285,7 +300,16 @@ function _normalizeStepIn(raw) {
     }
     return result;
 }
-function _normalizeStepOut(raw) {
+/**
+ * Expand a step's raw `out` value into normalized `{id, ...}` entries, covering
+ * every gxformat2 shorthand:
+ *   - list of strings:   out: [out_file1]             → {id: "out_file1"}
+ *   - list of objects:   out: [{id: out_file1, ...}]  → {id: "out_file1", ...}
+ *   - map:               out: {out_file1: {...}}      → {id: "out_file1", ...}
+ *
+ * Pure and value-based — see {@link normalizeStepIn}.
+ */
+export function normalizeStepOut(raw) {
     if (!raw)
         return [];
     if (Array.isArray(raw)) {

package/dist/workflow/normalized/format2.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/index.d.ts

@@ -1,4 +1,4 @@
-export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, } from "./format2.js";
 export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, } from "./native.js";
 export { toFormat2, type ToFormat2Options, type Format2StateOverride } from "./toFormat2.js";
 export { toNative, type ToNativeOptions } from "./toNative.js";

package/dist/workflow/normalized/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B,GACjC,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa,GACnB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAE,KAAK,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAE,KAAK,eAAe,EAAE,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB,GACxB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB,GACtB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EAAE,sBAAsB,EAAE,sBAAsB,EAAE,qBAAqB,EAAE,MAAM,aAAa,CAAC"}

package/dist/workflow/normalized/index.js

@@ -1,4 +1,4 @@
-export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, } from "./format2.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, } from "./format2.js";
 export { normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, } from "./native.js";
 export { toFormat2 } from "./toFormat2.js";
 export { toNative } from "./toNative.js";

package/dist/workflow/normalized/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/workflow/normalized/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,GAOlC,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,GAIpB,MAAM,aAAa,CAAC;AAErB,OAAO,EAAE,SAAS,EAAoD,MAAM,gBAAgB,CAAC;AAC7F,OAAO,EAAE,QAAQ,EAAwB,MAAM,eAAe,CAAC;AAC/D,OAAO,EACL,iBAAiB,GAIlB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,gBAAgB,EAA6B,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC1D,OAAO,EACL,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,GAOpB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACzE,OAAO,EAAE,sBAAsB,EAAE,sBAAsB,EAAE,qBAAqB,EAAE,MAAM,aAAa,CAAC"}

package/dist/workflow/report-models.d.ts

@@ -124,6 +124,13 @@ export interface DraftSurveyReport {
     todo_count: number;
     /** Distinct step paths carrying at least one TODO sentinel, in walk order. */
     todo_paths: string[][];
+    /**
+     * Distinct workflow-output locations carrying a TODO sentinel in their
+     * `outputSource`, in walk order. Each entry is `[...workflowPath, outputLabel]`
+     * — `["trimmed"]` for a root output, `["sub", "trimmed"]` for a subworkflow
+     * output. Kept separate from `todo_paths`: an output sentinel is not a step.
+     */
+    todo_output_paths: string[][];
     /** Distinct step paths carrying at least one `_plan_*` field, in walk order. */
     plan_step_paths: string[][];
 }

package/dist/workflow/report-models.d.ts.map

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package/dist/workflow/report-models.js

@@ -191,7 +191,18 @@ export function buildSingleDraftExtractReport(workflow, output, extract, promote
 function buildDraftSurveyReport(survey) {
     const todoSeen = new Set();
     const todoPaths = [];
+    const outputSeen = new Set();
+    const todoOutputPaths = [];
     for (const hit of survey.todos) {
+        if (hit.location.kind === "output_source") {
+            const outputPath = [...hit.path, hit.location.output_label];
+            const key = outputPath.join("/");
+            if (outputSeen.has(key))
+                continue;
+            outputSeen.add(key);
+            todoOutputPaths.push(outputPath);
+            continue;
+        }
         const key = hit.path.join("/");
         if (todoSeen.has(key))
             continue;
@@ -211,6 +222,7 @@ function buildDraftSurveyReport(survey) {
         is_draft: survey.isDraft,
         todo_count: survey.todos.length,
         todo_paths: todoPaths,
+        todo_output_paths: todoOutputPaths,
         plan_step_paths: planStepPaths,
     };
 }

package/dist/workflow/report-models.js.map

@@ -1 +1 @@
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package/dist/workflow/roundtrip.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/roundtrip.js

@@ -388,6 +388,76 @@ function collectSteps(wf, prefix = "", depth = 0) {
     }
     return { tools, subworkflows };
 }
+/**
+ * Map original tool-step ids onto their counterparts in the reimported workflow.
+ *
+ * format2 stores inputs separately from `steps`, so the reverse (format2→native)
+ * pass front-loads input steps and renumbers tools — a native step's numeric id
+ * is not stable across a roundtrip. Matching purely by id then compares unrelated
+ * steps. Mirrors Python's `_build_step_id_mapping` (`roundtrip.py`): match by
+ * label+type first, then same-id when the type matches, then a unique tool_id+type
+ * fallback for unlabeled steps that shifted position. Matching is scoped per
+ * nesting level (collected ids are parent-prefixed) so a subworkflow tool can't
+ * match a same-labeled top-level tool. Unmatched original steps map to `null`.
+ */
+function buildStepIdMapping(origSteps, afterSteps) {
+    const mapping = new Map();
+    const usedAfter = new Set();
+    const parentPrefix = (id) => id.includes(".") ? id.slice(0, id.lastIndexOf(".")) : "";
+    // Pass 1: label + type (strongest signal)
+    for (const [origId, { step: orig }] of origSteps) {
+        if (!orig.label)
+            continue;
+        for (const [afterId, { step: after }] of afterSteps) {
+            if (usedAfter.has(afterId))
+                continue;
+            if (parentPrefix(afterId) !== parentPrefix(origId))
+                continue;
+            if (after.label === orig.label && after.type === orig.type) {
+                mapping.set(origId, afterId);
+                usedAfter.add(afterId);
+                break;
+            }
+        }
+    }
+    // Pass 2: same id when the step type matches
+    for (const [origId, { step: orig }] of origSteps) {
+        if (mapping.has(origId))
+            continue;
+        const after = afterSteps.get(origId);
+        if (after && !usedAfter.has(origId) && after.step.type === orig.type) {
+            mapping.set(origId, origId);
+            usedAfter.add(origId);
+        }
+    }
+    // Pass 3: unique tool_id + type (unlabeled steps that shifted position)
+    for (const [origId, { step: orig }] of origSteps) {
+        if (mapping.has(origId))
+            continue;
+        if (!orig.tool_id)
+            continue;
+        const candidates = [];
+        for (const [afterId, { step: after }] of afterSteps) {
+            if (usedAfter.has(afterId))
+                continue;
+            if (parentPrefix(afterId) !== parentPrefix(origId))
+                continue;
+            if (after.tool_id === orig.tool_id && after.type === orig.type) {
+                candidates.push(afterId);
+            }
+        }
+        if (candidates.length === 1) {
+            mapping.set(origId, candidates[0]);
+            usedAfter.add(candidates[0]);
+        }
+    }
+    // Unmatched → null
+    for (const [origId] of origSteps) {
+        if (!mapping.has(origId))
+            mapping.set(origId, null);
+    }
+    return mapping;
+}
 // --- Public entry point ---
 /**
  * Roundtrip a native workflow through format2 and back, diffing each
@@ -512,9 +582,11 @@ export function roundtripValidate(nativeRaw, toolInputsResolver, strictOpts) {
         structureErrors.push(...checkStrictStructure(reimported, "native").map((e) => `reverse: ${e}`));
     }
     const { tools: reimportedSteps } = collectSteps(reimported);
+    const stepMapping = buildStepIdMapping(originalSteps, reimportedSteps);
     // Per-step comparison (top-level + recursively-collected nested tools)
     for (const [stepId, { step: origStep, depth }] of originalSteps) {
-        const afterEntry = reimportedSteps.get(stepId);
+        const afterId = stepMapping.get(stepId);
+        const afterEntry = afterId != null ? reimportedSteps.get(afterId) : undefined;
         if (!afterEntry) {
             stepResults.push({
                 stepId,

package/dist/workflow/roundtrip.js.map

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package/dist/workflow/serialize.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/serialize.js

@@ -6,6 +6,50 @@
  */
 import { stringify as stringifyYaml } from "yaml";
 import { detectFormat } from "./detect-format.js";
+/**
+ * In-memory-only fields derived during normalization (see
+ * `workflow/normalized/native.ts` and `format2.ts`). They are never part of
+ * the on-disk Galaxy format: `unique_tools` is a workflow-level `Set` of tool
+ * references, `connected_paths` is a per-step `Set` of input-connection keys.
+ * Serializing a `Set` yields `{}` (JSON) / an empty mapping (YAML), so left in
+ * place they leak as stray keys that downstream schema validators reject.
+ *
+ * Stripped structurally (workflow level / step level / subworkflows) rather
+ * than by a blanket recursive key match so a tool parameter that happens to be
+ * named `unique_tools`/`connected_paths` inside `tool_state` is preserved.
+ */
+function stripDerivedFields(data) {
+    return stripWorkflowDict(data);
+}
+function stripWorkflowDict(wf) {
+    const out = { ...wf };
+    delete out.unique_tools;
+    if (out.steps && typeof out.steps === "object") {
+        out.steps = stripSteps(out.steps);
+    }
+    return out;
+}
+function stripSteps(steps) {
+    if (Array.isArray(steps))
+        return steps.map(stripStep);
+    const out = {};
+    for (const [key, value] of Object.entries(steps))
+        out[key] = stripStep(value);
+    return out;
+}
+function stripStep(step) {
+    if (step == null || typeof step !== "object")
+        return step;
+    const out = { ...step };
+    delete out.connected_paths;
+    // Embedded subworkflows: `subworkflow` (native) / `run` (format2).
+    for (const key of ["subworkflow", "run"]) {
+        if (out[key] && typeof out[key] === "object") {
+            out[key] = stripWorkflowDict(out[key]);
+        }
+    }
+    return out;
+}
 /**
  * Serialize a workflow dict as JSON or YAML based on `format` (or explicit
  * `json` / `yaml` overrides).
@@ -19,6 +63,7 @@ import { detectFormat } from "./detect-format.js";
  * reader decode them as booleans. Real numbers/booleans are unaffected.
  */
 export function serializeWorkflow(data, format, opts = {}) {
+    data = stripDerivedFields(data);
     const useYaml = opts.yaml || (!opts.json && format === "format2");
     const newline = opts.trailingNewline ?? true;
     if (useYaml) {

package/dist/workflow/serialize.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.7.2",
+  "version": "1.8.2",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {