@galaxy-tool-util/schema 1.10.1 → 1.13.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (104) hide show
  1. package/dist/index.d.ts +29 -4
  2. package/dist/index.d.ts.map +1 -1
  3. package/dist/index.js +23 -2
  4. package/dist/index.js.map +1 -1
  5. package/dist/schema/bundle-types.d.ts +6 -2
  6. package/dist/schema/bundle-types.d.ts.map +1 -1
  7. package/dist/schema/bundle-types.js.map +1 -1
  8. package/dist/schema/parameter-defaults.d.ts.map +1 -1
  9. package/dist/schema/parameter-defaults.js +7 -3
  10. package/dist/schema/parameter-defaults.js.map +1 -1
  11. package/dist/schema/parameters/base.d.ts.map +1 -1
  12. package/dist/schema/parameters/base.js +3 -1
  13. package/dist/schema/parameters/base.js.map +1 -1
  14. package/dist/schema/parameters/gx-drill-down.js +2 -1
  15. package/dist/schema/parameters/gx-drill-down.js.map +1 -1
  16. package/dist/schema/parameters/gx-text.js +2 -2
  17. package/dist/schema/parameters/gx-text.js.map +1 -1
  18. package/dist/schema/parsed-tool.d.ts +180 -10
  19. package/dist/schema/parsed-tool.d.ts.map +1 -1
  20. package/dist/schema/parsed-tool.js +56 -2
  21. package/dist/schema/parsed-tool.js.map +1 -1
  22. package/dist/schema/state-representations.js +1 -1
  23. package/dist/schema/state-representations.js.map +1 -1
  24. package/dist/tool-state-validator.d.ts +2 -2
  25. package/dist/tool-state-validator.d.ts.map +1 -1
  26. package/dist/tool-state-validator.js +4 -4
  27. package/dist/tool-state-validator.js.map +1 -1
  28. package/dist/trs/index.d.ts +110 -0
  29. package/dist/trs/index.d.ts.map +1 -0
  30. package/dist/trs/index.js +64 -0
  31. package/dist/trs/index.js.map +1 -0
  32. package/dist/user-tool-parse/index.d.ts +4 -1
  33. package/dist/user-tool-parse/index.d.ts.map +1 -1
  34. package/dist/user-tool-parse/index.js +4 -1
  35. package/dist/user-tool-parse/index.js.map +1 -1
  36. package/dist/user-tool-parse/input-source.d.ts +105 -0
  37. package/dist/user-tool-parse/input-source.d.ts.map +1 -0
  38. package/dist/user-tool-parse/input-source.js +271 -0
  39. package/dist/user-tool-parse/input-source.js.map +1 -0
  40. package/dist/user-tool-parse/inputs.d.ts +15 -8
  41. package/dist/user-tool-parse/inputs.d.ts.map +1 -1
  42. package/dist/user-tool-parse/inputs.js +188 -295
  43. package/dist/user-tool-parse/inputs.js.map +1 -1
  44. package/dist/user-tool-parse/outputs.d.ts +2 -1
  45. package/dist/user-tool-parse/outputs.d.ts.map +1 -1
  46. package/dist/user-tool-parse/outputs.js +4 -3
  47. package/dist/user-tool-parse/outputs.js.map +1 -1
  48. package/dist/user-tool-parse/parse.d.ts +17 -2
  49. package/dist/user-tool-parse/parse.d.ts.map +1 -1
  50. package/dist/user-tool-parse/parse.js +23 -6
  51. package/dist/user-tool-parse/parse.js.map +1 -1
  52. package/dist/workflow/cytoscape.d.ts.map +1 -1
  53. package/dist/workflow/cytoscape.js +5 -3
  54. package/dist/workflow/cytoscape.js.map +1 -1
  55. package/dist/workflow/draft-checks.d.ts +2 -1
  56. package/dist/workflow/draft-checks.d.ts.map +1 -1
  57. package/dist/workflow/draft-checks.js +29 -5
  58. package/dist/workflow/draft-checks.js.map +1 -1
  59. package/dist/workflow/index.d.ts +1 -1
  60. package/dist/workflow/index.d.ts.map +1 -1
  61. package/dist/workflow/index.js +1 -1
  62. package/dist/workflow/index.js.map +1 -1
  63. package/dist/workflow/mermaid.d.ts +1 -1
  64. package/dist/workflow/mermaid.d.ts.map +1 -1
  65. package/dist/workflow/mermaid.js +5 -3
  66. package/dist/workflow/mermaid.js.map +1 -1
  67. package/dist/workflow/normalized/expanded.d.ts.map +1 -1
  68. package/dist/workflow/normalized/expanded.js +8 -2
  69. package/dist/workflow/normalized/expanded.js.map +1 -1
  70. package/dist/workflow/normalized/format2.d.ts +22 -1
  71. package/dist/workflow/normalized/format2.d.ts.map +1 -1
  72. package/dist/workflow/normalized/format2.js +26 -5
  73. package/dist/workflow/normalized/format2.js.map +1 -1
  74. package/dist/workflow/normalized/index.d.ts +1 -1
  75. package/dist/workflow/normalized/index.d.ts.map +1 -1
  76. package/dist/workflow/normalized/index.js +1 -1
  77. package/dist/workflow/normalized/index.js.map +1 -1
  78. package/dist/workflow/normalized/stateful-runner.d.ts +3 -1
  79. package/dist/workflow/normalized/stateful-runner.d.ts.map +1 -1
  80. package/dist/workflow/normalized/stateful-runner.js +1 -1
  81. package/dist/workflow/normalized/stateful-runner.js.map +1 -1
  82. package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
  83. package/dist/workflow/normalized/toFormat2.js +34 -11
  84. package/dist/workflow/normalized/toFormat2.js.map +1 -1
  85. package/dist/workflow/normalized/toFormat2Stateful.js +8 -10
  86. package/dist/workflow/normalized/toFormat2Stateful.js.map +1 -1
  87. package/dist/workflow/normalized/toNative.d.ts.map +1 -1
  88. package/dist/workflow/normalized/toNative.js +16 -26
  89. package/dist/workflow/normalized/toNative.js.map +1 -1
  90. package/dist/workflow/normalized/toNativeStateful.d.ts.map +1 -1
  91. package/dist/workflow/normalized/toNativeStateful.js +3 -10
  92. package/dist/workflow/normalized/toNativeStateful.js.map +1 -1
  93. package/dist/workflow/report-models.d.ts +1 -1
  94. package/dist/workflow/report-models.d.ts.map +1 -1
  95. package/dist/workflow/report-models.js +1 -0
  96. package/dist/workflow/report-models.js.map +1 -1
  97. package/dist/workflow/stateful-convert.d.ts.map +1 -1
  98. package/dist/workflow/stateful-convert.js +6 -0
  99. package/dist/workflow/stateful-convert.js.map +1 -1
  100. package/dist/workflow/stateful-validate.d.ts +12 -5
  101. package/dist/workflow/stateful-validate.d.ts.map +1 -1
  102. package/dist/workflow/stateful-validate.js +62 -24
  103. package/dist/workflow/stateful-validate.js.map +1 -1
  104. package/package.json +1 -1
package/dist/workflow/draft-checks.js.map CHANGED
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package/dist/workflow/index.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  export { serializeWorkflow, resolveFormat, type SerializeWorkflowOptions } from "./serialize.js";
2
2
  export { type GalaxyWorkflow, GalaxyWorkflowSchema, type GalaxyWorkflowDraft, GalaxyWorkflowDraftSchema, type DraftWorkflowStep, DraftWorkflowStepSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
3
3
  export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
4
- 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
4
+ export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, type GalaxyUserToolStub, 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
5
5
  export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
6
6
  export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
7
7
  export { expandToolStateDefaults } from "./fill-defaults.js";
package/dist/workflow/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/dist/workflow/index.js CHANGED
@@ -5,7 +5,7 @@ export { GalaxyWorkflowSchema, GalaxyWorkflowDraftSchema, DraftWorkflowStepSchem
5
5
  // Plain JSON Schema siblings for downstream packagers (issue #108)
6
6
  export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
7
7
  // Normalized workflow types + normalizers
8
- 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
8
+ export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
9
9
  export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
10
10
  export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
11
11
  export { expandToolStateDefaults } from "./fill-defaults.js";
package/dist/workflow/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/workflow/index.ts"],"names":[],"mappings":"AAAA,qCAAqC;AACrC,OAAO,EAAE,iBAAiB,EAAE,aAAa,EAAiC,MAAM,gBAAgB,CAAC;AAEjG,wCAAwC;AACxC,OAAO,EAEL,oBAAoB,EAEpB,yBAAyB,EAEzB,uBAAuB,EAEvB,0BAA0B,GAC3B,MAAM,gBAAgB,CAAC;AAExB,mEAAmE;AACnE,OAAO,EAAE,6BAA6B,EAAE,MAAM,mBAAmB,CAAC;AAElE,0CAA0C;AAC1C,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EAOjC,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EAInB,SAAS,EAGT,QAAQ,EAER,iBAAiB,EACjB,gBAAgB,EAMhB,aAAa,EACb,YAAY,EACZ,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EAOnB,kBAAkB,EAClB,oBAAoB,EACpB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,mBAAmB,CAAC;AAE3B,OAAO,EACL,0BAA0B,EAC1B,oBAAoB,EACpB,8BAA8B,GAC/B,MAAM,kBAAkB,CAAC;AAE1B,OAAO,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAC;AAChE,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,SAAS,GAEV,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EAAE,mBAAmB,EAAkC,MAAM,uBAAuB,CAAC;AAE5F,OAAO,EACL,aAAa,GAId,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,UAAU,EACV,eAAe,EACf,oBAAoB,GAGrB,MAAM,aAAa,CAAC;AAErB,OAAO,EACL,kBAAkB,EAClB,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,GAEpB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,sBAAsB,EACtB,kBAAkB,GAGnB,MAAM,eAAe,CAAC;AAEvB,OAAO,EACL,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB,EACxB,8BAA8B,GAG/B,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,eAAe,EAA8B,MAAM,uBAAuB,CAAC;AAEpF,OAAO,EACL,iBAAiB,GAMlB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EAAE,aAAa,EAAuD,MAAM,YAAY,CAAC;AAEhG,OAAO,EAAE,iBAAiB,EAAuB,MAAM,cAAc,CAAC;AAEtE,OAAO,EAAE,iBAAiB,EAAuB,MAAM,sBAAsB,CAAC;AAE9E,OAAO,EAAE,iBAAiB,EAAyB,MAAM,gBAAgB,CAAC;AAC1E,OAAO,EACL,cAAc,GAUf,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,UAAU,EACV,YAAY,EACZ,gBAAgB,EAChB,YAAY,EACZ,oBAAoB,GAErB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,YAAY,EAAuB,MAAM,oBAAoB,CAAC;AAEvE,OAAO,EACL,qBAAqB,EACrB,WAAW,EACX,WAAW,EACX,cAAc,EACd,eAAe,EACf,WAAW,EACX,aAAa,EACb,aAAa,EACb,qBAAqB,EACrB,mBAAmB,EACnB,aAAa,GAiBd,MAAM,mBAAmB,CAAC;AAE3B,OAAO,EACL,eAAe,EACf,0BAA0B,GAI3B,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,SAAS,EACT,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,GACpB,MAAM,iBAAiB,CAAC;AAEzB,OAAO,EACL,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB,EACnB,oBAAoB,GACrB,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,UAAU,EACV,WAAW,EACX,YAAY,EACZ,wBAAwB,EACxB,uBAAuB,GAKxB,MAAM,WAAW,CAAC;AAEnB,OAAO,EAAE,uBAAuB,EAAE,MAAM,iBAAiB,CAAC;AAE1D,OAAO,EACL,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB,GAElB,MAAM,oBAAoB,CAAC;AAE5B,8DAA8D;AAC9D,OAAO,EAEL,aAAa,EAwDb,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,GACzB,MAAM,oBAAoB,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/workflow/index.ts"],"names":[],"mappings":"AAAA,qCAAqC;AACrC,OAAO,EAAE,iBAAiB,EAAE,aAAa,EAAiC,MAAM,gBAAgB,CAAC;AAEjG,wCAAwC;AACxC,OAAO,EAEL,oBAAoB,EAEpB,yBAAyB,EAEzB,uBAAuB,EAEvB,0BAA0B,GAC3B,MAAM,gBAAgB,CAAC;AAExB,mEAAmE;AACnE,OAAO,EAAE,6BAA6B,EAAE,MAAM,mBAAmB,CAAC;AAElE,0CAA0C;AAC1C,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,wBAAwB,EACxB,mBAAmB,EAQnB,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EAInB,SAAS,EAGT,QAAQ,EAER,iBAAiB,EACjB,gBAAgB,EAMhB,aAAa,EACb,YAAY,EACZ,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EAOnB,kBAAkB,EAClB,oBAAoB,EACpB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EACrB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,mBAAmB,CAAC;AAE3B,OAAO,EACL,0BAA0B,EAC1B,oBAAoB,EACpB,8BAA8B,GAC/B,MAAM,kBAAkB,CAAC;AAE1B,OAAO,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAC;AAChE,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,SAAS,GAEV,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EAAE,mBAAmB,EAAkC,MAAM,uBAAuB,CAAC;AAE5F,OAAO,EACL,aAAa,GAId,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,UAAU,EACV,eAAe,EACf,oBAAoB,GAGrB,MAAM,aAAa,CAAC;AAErB,OAAO,EACL,kBAAkB,EAClB,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,GAEpB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,sBAAsB,EACtB,kBAAkB,GAGnB,MAAM,eAAe,CAAC;AAEvB,OAAO,EACL,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB,EACxB,8BAA8B,GAG/B,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EAAE,eAAe,EAA8B,MAAM,uBAAuB,CAAC;AAEpF,OAAO,EACL,iBAAiB,GAMlB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EAAE,aAAa,EAAuD,MAAM,YAAY,CAAC;AAEhG,OAAO,EAAE,iBAAiB,EAAuB,MAAM,cAAc,CAAC;AAEtE,OAAO,EAAE,iBAAiB,EAAuB,MAAM,sBAAsB,CAAC;AAE9E,OAAO,EAAE,iBAAiB,EAAyB,MAAM,gBAAgB,CAAC;AAC1E,OAAO,EACL,cAAc,GAUf,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,UAAU,EACV,YAAY,EACZ,gBAAgB,EAChB,YAAY,EACZ,oBAAoB,GAErB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,YAAY,EAAuB,MAAM,oBAAoB,CAAC;AAEvE,OAAO,EACL,qBAAqB,EACrB,WAAW,EACX,WAAW,EACX,cAAc,EACd,eAAe,EACf,WAAW,EACX,aAAa,EACb,aAAa,EACb,qBAAqB,EACrB,mBAAmB,EACnB,aAAa,GAiBd,MAAM,mBAAmB,CAAC;AAE3B,OAAO,EACL,eAAe,EACf,0BAA0B,GAI3B,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,SAAS,EACT,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,GACpB,MAAM,iBAAiB,CAAC;AAEzB,OAAO,EACL,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB,EACnB,oBAAoB,GACrB,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,UAAU,EACV,WAAW,EACX,YAAY,EACZ,wBAAwB,EACxB,uBAAuB,GAKxB,MAAM,WAAW,CAAC;AAEnB,OAAO,EAAE,uBAAuB,EAAE,MAAM,iBAAiB,CAAC;AAE1D,OAAO,EACL,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB,GAElB,MAAM,oBAAoB,CAAC;AAE5B,8DAA8D;AAC9D,OAAO,EAEL,aAAa,EAwDb,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,GACzB,MAAM,oBAAoB,CAAC"}
package/dist/workflow/mermaid.d.ts CHANGED
@@ -5,7 +5,7 @@
5
5
  */
6
6
  import type { DraftOverlay } from "./draft-checks.js";
7
7
  import type { EdgeAnnotation } from "./edge-annotation.js";
8
- import type { NormalizedFormat2Workflow } from "./normalized/format2.js";
8
+ import { type NormalizedFormat2Workflow } from "./normalized/format2.js";
9
9
  export interface MermaidOptions {
10
10
  comments?: boolean;
11
11
  /**
package/dist/workflow/mermaid.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6BzE,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAuJR"}
1
+ {"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAAuB,KAAK,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6B9F,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAwJR"}
package/dist/workflow/mermaid.js CHANGED
@@ -6,6 +6,7 @@
6
6
  import { isDraftWorkflow, isTodoSentinel, PLANNED_CLASS, resolveDraftOverlay, } from "./draft-checks.js";
7
7
  import { edgeAnnotationKey } from "./edge-annotation.js";
8
8
  import { ensureFormat2 } from "./normalized/ensure.js";
9
+ import { isGalaxyUserToolRun } from "./normalized/format2.js";
9
10
  import { isUnlabeledStep, resolveSourceReference, stepRenderIdentity, } from "./normalized/labels.js";
10
11
  const SHAPE_INPUT = [">", "]"];
11
12
  const SHAPE_PARAM = ["{{", "}}"];
@@ -118,9 +119,10 @@ export function workflowToMermaid(workflow, opts = {}) {
118
119
  const displayId = step.id && !isUnlabeledStep(step.id) ? step.id : null;
119
120
  const rawLabel = step.label || displayId || (toolId ? `tool:${toolId}` : String(i));
120
121
  const label = sanitizeLabel(rawLabel);
121
- // The TS normalizer does not infer step.type the way gxformat2 does, so
122
- // fall back to `run` shape: anything non-null implies a subworkflow.
123
- const stepType = step.type || (step.run != null ? "subworkflow" : "tool");
122
+ // An embedded GalaxyUserTool run is a tool, while workflow runs are subworkflows.
123
+ const stepType = isGalaxyUserToolRun(step.run)
124
+ ? "tool"
125
+ : step.type || (step.run != null ? "subworkflow" : "tool");
124
126
  const shape = STEP_TYPE_SHAPES[stepType] ?? SHAPE_TOOL;
125
127
  stepLines.set(stepLabel, nodeLine(nodeId, label, shape));
126
128
  });
package/dist/workflow/mermaid.js.map CHANGED
@@ -1 +1 @@
1
- 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+ {"version":3,"file":"expanded.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/expanded.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAEV,yBAAyB,EACzB,qBAAqB,EACtB,MAAM,cAAc,CAAC;AAEtB,OAAO,KAAK,EAAE,wBAAwB,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAUlF,MAAM,MAAM,uBAAuB,GAAG,yBAAyB,CAAC;AAChE,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AACxD,MAAM,MAAM,sBAAsB,GAAG,wBAAwB,CAAC;AAC9D,MAAM,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEtD;;;;;;;;GAQG;AACH,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;AAE5E;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,WAAW,CAAC;CACxB;AAID,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAMtC,sEAAsE;AACtE,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE7C;AA8DD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,uBAAuB,CAAC,CAQlC;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAClC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,gBAAgB,GACzB,OAAO,CAAC,sBAAsB,CAAC,CAQjC"}
package/dist/workflow/normalized/expanded.js CHANGED
@@ -8,7 +8,7 @@
8
8
  * Port of gxformat2/normalized/_conversion.py expanded_format2/expanded_native
9
9
  * and gxformat2/options.py (UrlResolverFn, default_url_resolver, ConversionOptions).
10
10
  */
11
- import { normalizedFormat2 } from "./format2.js";
11
+ import { isGalaxyUserToolRun, normalizedFormat2 } from "./format2.js";
12
12
  import { normalizedNative } from "./native.js";
13
13
  import { toFormat2 } from "./toFormat2.js";
14
14
  import { toNative } from "./toNative.js";
@@ -102,6 +102,8 @@ export async function expandedNative(raw, options) {
102
102
  // --- Sync expansion (no resolver — inline subworkflows only) ---
103
103
  function _expandFormat2Sync(wf) {
104
104
  const expandedSteps = wf.steps.map((step) => {
105
+ if (isGalaxyUserToolRun(step.run))
106
+ return step;
105
107
  if (step.run && typeof step.run === "object") {
106
108
  return { ...step, run: _expandFormat2Sync(step.run) };
107
109
  }
@@ -126,7 +128,11 @@ async function _expandFormat2(wf, ctx) {
126
128
  const expandedSteps = [];
127
129
  for (const step of wf.steps) {
128
130
  let expandedRun = null;
129
- if (step.run && typeof step.run === "object") {
131
+ if (isGalaxyUserToolRun(step.run)) {
132
+ // Embedded user-defined tool — nothing to resolve
133
+ expandedRun = step.run;
134
+ }
135
+ else if (step.run && typeof step.run === "object") {
130
136
  // Already-inlined subworkflow — recurse
131
137
  expandedRun = await _expandFormat2(step.run, ctx);
132
138
  }
package/dist/workflow/normalized/expanded.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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AC;YAC5C,MAAM,UAAU,GAAG,aAAa,CAAC,QAAQ,CAAC,CAAC;YAC3C,WAAW,GAAG,MAAM,aAAa,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;QAC1D,CAAC;QAED,IAAI,WAAW,IAAI,IAAI,EAAE,CAAC;YACxB,6CAA6C;YAC7C,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAC;YAC/C,aAAa,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,aAAa,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;QAC5B,CAAC;IACH,CAAC;IAED,OAAO,EAAE,GAAG,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC;AACzC,CAAC"}
package/dist/workflow/normalized/format2.d.ts CHANGED
@@ -32,6 +32,8 @@ export declare const NormalizedFormat2InputSchema: Schema.Struct<{
32
32
  type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
33
33
  optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
34
34
  default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
35
+ min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
36
+ max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
35
37
  format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
36
38
  collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
37
39
  position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -45,6 +47,18 @@ export declare const NormalizedFormat2OutputSchema: Schema.Struct<{
45
47
  type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
46
48
  }>;
47
49
  export type NormalizedFormat2Output = typeof NormalizedFormat2OutputSchema.Type;
50
+ /**
51
+ * An embedded user-defined tool under a step's `run:` (`class: GalaxyUserTool`).
52
+ * Only the discriminator is modelled; the rest of the tool definition passes
53
+ * through untouched. Mirrors gxformat2's `GalaxyUserToolStub`.
54
+ */
55
+ export declare const GalaxyUserToolStubSchema: Schema.TypeLiteral<{
56
+ class: Schema.Literal<["GalaxyUserTool"]>;
57
+ name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
58
+ }, readonly [Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>;
59
+ export type GalaxyUserToolStub = typeof GalaxyUserToolStubSchema.Type;
60
+ /** True when a step's `run:` embeds a user-defined tool rather than a subworkflow. */
61
+ export declare function isGalaxyUserToolRun(run: unknown): run is GalaxyUserToolStub;
48
62
  export declare const NormalizedFormat2WorkflowSchema: Schema.Struct<{
49
63
  class: Schema.Literal<["GalaxyWorkflow"]>;
50
64
  label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
@@ -56,6 +70,8 @@ export declare const NormalizedFormat2WorkflowSchema: Schema.Struct<{
56
70
  type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
57
71
  optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
58
72
  default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
73
+ min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
74
+ max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
59
75
  format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
60
76
  collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
61
77
  position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -98,6 +114,8 @@ export declare const NormalizedFormat2StepSchema: Schema.Struct<{
98
114
  type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
99
115
  optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
100
116
  default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
117
+ min: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
118
+ max: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
101
119
  format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
102
120
  collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
103
121
  position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
@@ -119,7 +137,10 @@ export declare const NormalizedFormat2StepSchema: Schema.Struct<{
119
137
  tool_id: typeof Schema.String;
120
138
  tool_version: Schema.NullOr<typeof Schema.String>;
121
139
  }>>;
122
- }>, typeof Schema.String]>>>;
140
+ }>, Schema.TypeLiteral<{
141
+ class: Schema.Literal<["GalaxyUserTool"]>;
142
+ name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
143
+ }, readonly [Schema.Record$<typeof Schema.String, typeof Schema.Unknown>]>, typeof Schema.String]>>>;
123
144
  in: Schema.Array$<Schema.Struct<{
124
145
  id: typeof Schema.String;
125
146
  source: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
package/dist/workflow/normalized/format2.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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"}
1
+ {"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;;;;;;;;;;;;EAcvC,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;AAEhF;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;0EAMpC,CAAC;AACF,MAAM,MAAM,kBAAkB,GAAG,OAAO,wBAAwB,CAAC,IAAI,CAAC;AAEtE,sFAAsF;AACtF,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,OAAO,GAAG,GAAG,IAAI,kBAAkB,CAO3E;AAGD,eAAO,MAAM,+BAA+B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAe1C,CAAC;AACH,MAAM,MAAM,yBAAyB,GAAG,OAAO,+BAA+B,CAAC,IAAI,CAAC;AAEpF,eAAO,MAAM,2BAA2B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiCtC,CAAC;AACH,MAAM,MAAM,qBAAqB,GAAG,OAAO,2BAA2B,CAAC,IAAI,CAAC;AAI5E,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,OAAO,GAAG,yBAAyB,CAsBzE;AAyKD;;;;;;;;;;;;;;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 CHANGED
@@ -42,6 +42,8 @@ export const NormalizedFormat2InputSchema = Schema.Struct({
42
42
  type: Schema.optional(Schema.NullOr(Schema.Union(Schema.String, Schema.Array(Schema.String)))),
43
43
  optional: Schema.optional(Schema.NullOr(Schema.Boolean)),
44
44
  default: Schema.optional(Schema.NullOr(Schema.Unknown)),
45
+ min: Schema.optional(Schema.NullOr(Schema.Number)),
46
+ max: Schema.optional(Schema.NullOr(Schema.Number)),
45
47
  format: Schema.optional(Schema.NullOr(Schema.Array(Schema.String))),
46
48
  collection_type: Schema.optional(Schema.NullOr(Schema.String)),
47
49
  position: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
@@ -53,6 +55,22 @@ export const NormalizedFormat2OutputSchema = Schema.Struct({
53
55
  outputSource: Schema.optional(Schema.NullOr(Schema.String)),
54
56
  type: Schema.optional(Schema.NullOr(Schema.String)),
55
57
  });
58
+ /**
59
+ * An embedded user-defined tool under a step's `run:` (`class: GalaxyUserTool`).
60
+ * Only the discriminator is modelled; the rest of the tool definition passes
61
+ * through untouched. Mirrors gxformat2's `GalaxyUserToolStub`.
62
+ */
63
+ export const GalaxyUserToolStubSchema = Schema.Struct({
64
+ class: Schema.Literal("GalaxyUserTool"),
65
+ name: Schema.optional(Schema.NullOr(Schema.String)),
66
+ }, Schema.Record({ key: Schema.String, value: Schema.Unknown }));
67
+ /** True when a step's `run:` embeds a user-defined tool rather than a subworkflow. */
68
+ export function isGalaxyUserToolRun(run) {
69
+ return (run != null &&
70
+ typeof run === "object" &&
71
+ !Array.isArray(run) &&
72
+ run.class === "GalaxyUserTool");
73
+ }
56
74
  // Workflow defined first; step uses suspend for forward ref
57
75
  export const NormalizedFormat2WorkflowSchema = Schema.Struct({
58
76
  class: Schema.Literal("GalaxyWorkflow"),
@@ -76,7 +94,7 @@ export const NormalizedFormat2StepSchema = Schema.Struct({
76
94
  tool_version: Schema.optional(Schema.NullOr(Schema.String)),
77
95
  tool_shed_repository: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
78
96
  type: Schema.optional(Schema.NullOr(Schema.String)),
79
- run: Schema.optional(Schema.NullOr(Schema.Union(NormalizedFormat2WorkflowSchema, Schema.String))),
97
+ run: Schema.optional(Schema.NullOr(Schema.Union(NormalizedFormat2WorkflowSchema, GalaxyUserToolStubSchema, Schema.String))),
80
98
  in: Schema.Array(NormalizedFormat2StepInputSchema),
81
99
  out: Schema.Array(NormalizedFormat2StepOutputSchema),
82
100
  post_job_actions: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
@@ -115,7 +133,7 @@ export function normalizedFormat2(raw) {
115
133
  function _normalizeWorkflow(raw, subworkflows) {
116
134
  const inputs = _normalizeInputs(raw.inputs);
117
135
  const outputs = _normalizeOutputs(raw.outputs);
118
- const steps = _normalizeSteps(raw.steps, subworkflows);
136
+ const steps = _normalizeSteps(raw.steps, subworkflows, inputs.length);
119
137
  const uniqueTools = _collectUniqueTools(steps);
120
138
  const result = {
121
139
  class: "GalaxyWorkflow",
@@ -189,13 +207,16 @@ function _normalizeOutputs(raw) {
189
207
  }
190
208
  return result;
191
209
  }
192
- function _normalizeSteps(raw, subworkflows) {
210
+ function _normalizeSteps(raw, subworkflows, inputsOffset = 0) {
193
211
  if (!raw)
194
212
  return [];
195
213
  if (Array.isArray(raw)) {
214
+ // List-form steps without an explicit id get the index they will occupy in
215
+ // native form, where inputs come first -- so a numeric source like
216
+ // "1/out_file1" means the same thing before and after conversion.
196
217
  return raw.map((item, idx) => {
197
218
  const obj = item;
198
- return _normalizeStep(obj, obj.id ?? String(idx), subworkflows);
219
+ return _normalizeStep(obj, obj.id ?? String(idx + inputsOffset), subworkflows);
199
220
  });
200
221
  }
201
222
  const result = [];
@@ -355,7 +376,7 @@ function _resolveRun(raw, subworkflows) {
355
376
  return dict["@import"];
356
377
  }
357
378
  // User-defined tool — pass through as-is
358
- if (dict.class === "GalaxyUserTool") {
379
+ if (isGalaxyUserToolRun(dict)) {
359
380
  return dict;
360
381
  }
361
382
  // Inline workflow definition