@galaxy-tool-util/schema 0.4.0 → 1.1.0
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.
- package/dist/index.d.ts +13 -2
- package/dist/index.d.ts.map +1 -1
- package/dist/index.js +12 -1
- package/dist/index.js.map +1 -1
- package/dist/schema/parameter-defaults.d.ts +36 -0
- package/dist/schema/parameter-defaults.d.ts.map +1 -0
- package/dist/schema/parameter-defaults.js +128 -0
- package/dist/schema/parameter-defaults.js.map +1 -0
- package/dist/schema/parsed-tool.d.ts +47 -0
- package/dist/schema/parsed-tool.d.ts.map +1 -0
- package/dist/schema/parsed-tool.js +49 -0
- package/dist/schema/parsed-tool.js.map +1 -0
- package/dist/test-format/tests.schema.generated.d.ts +619 -459
- package/dist/test-format/tests.schema.generated.d.ts.map +1 -1
- package/dist/test-format/tests.schema.generated.js +738 -546
- package/dist/test-format/tests.schema.generated.js.map +1 -1
- package/dist/tool-state-validator.d.ts +11 -4
- package/dist/tool-state-validator.d.ts.map +1 -1
- package/dist/tool-state-validator.js +2 -2
- package/dist/tool-state-validator.js.map +1 -1
- package/dist/workflow/fill-defaults.d.ts +39 -0
- package/dist/workflow/fill-defaults.d.ts.map +1 -0
- package/dist/workflow/fill-defaults.js +53 -0
- package/dist/workflow/fill-defaults.js.map +1 -0
- package/dist/workflow/index.d.ts +4 -0
- package/dist/workflow/index.d.ts.map +1 -1
- package/dist/workflow/index.js +4 -0
- package/dist/workflow/index.js.map +1 -1
- package/dist/workflow/mermaid.d.ts +11 -0
- package/dist/workflow/mermaid.d.ts.map +1 -0
- package/dist/workflow/mermaid.js +158 -0
- package/dist/workflow/mermaid.js.map +1 -0
- package/dist/workflow/minimal-tool-state.d.ts +15 -0
- package/dist/workflow/minimal-tool-state.d.ts.map +1 -0
- package/dist/workflow/minimal-tool-state.js +16 -0
- package/dist/workflow/minimal-tool-state.js.map +1 -0
- package/dist/workflow/report-models.d.ts +4 -0
- package/dist/workflow/report-models.d.ts.map +1 -1
- package/dist/workflow/report-models.js +2 -0
- package/dist/workflow/report-models.js.map +1 -1
- package/dist/workflow/step-skeleton.d.ts +29 -0
- package/dist/workflow/step-skeleton.d.ts.map +1 -0
- package/dist/workflow/step-skeleton.js +55 -0
- package/dist/workflow/step-skeleton.js.map +1 -0
- package/dist/workflow/walker.d.ts +10 -0
- package/dist/workflow/walker.d.ts.map +1 -1
- package/dist/workflow/walker.js +16 -7
- package/dist/workflow/walker.js.map +1 -1
- package/package.json +2 -4
package/dist/workflow/walker.js
CHANGED
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@@ -33,6 +33,7 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
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const prefix = options?.prefix;
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const checkUnknownKeys = options?.checkUnknownKeys ?? false;
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const preserveUnknownKeys = options?.preserveUnknownKeys ?? false;
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+
const repeatMinPad = options?.repeatMinPad ?? false;
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const result = {};
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const visitedKeys = new Set();
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for (const toolInput of toolInputs) {
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@@ -48,7 +49,7 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
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const when = selectWhichWhen(conditional, stateDict);
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const branchParams = when != null ? when.parameters : [];
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// Walk the test parameter + branch parameters
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const innerResult = walkNativeState(inputConnections, [conditional.test_parameter, ...branchParams], stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys });
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const innerResult = walkNativeState(inputConnections, [conditional.test_parameter, ...branchParams], stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
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if (Object.keys(innerResult).length > 0) {
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result[name] = innerResult;
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}
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@@ -61,17 +62,25 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
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const stateArray = Array.isArray(repeatState)
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? repeatState
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: [];
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let instanceCount;
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if (repeatMinPad) {
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instanceCount = Math.max(stateArray.length, repeat.min ?? 0);
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}
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else {
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const connectionInstances = repeatInputsToArray(statePath, inputConnections);
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instanceCount = Math.max(stateArray.length, connectionInstances.length);
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}
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const instances = [];
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for (let i = 0; i < instanceCount; i++) {
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const instanceState = stateArray[i] ?? {};
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const instancePrefix = `${statePath}_${i}`;
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const instanceResult = walkNativeState(inputConnections, repeat.parameters, instanceState, leafCallback, { prefix: instancePrefix, checkUnknownKeys, preserveUnknownKeys });
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const instanceResult = walkNativeState(inputConnections, repeat.parameters, instanceState, leafCallback, { prefix: instancePrefix, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
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instances.push(instanceResult);
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}
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// Preserve explicit empty arrays (valid state); omit only when key is absent
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// Preserve explicit empty arrays (valid state); omit only when key is absent.
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// In repeatMinPad mode (expand-defaults), always write the key — mirrors
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// Python's _initialize_repeat_state which creates tool_state[name] = [].
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if (repeatMinPad || name in state || instances.length > 0) {
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result[name] = instances;
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}
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}
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@@ -80,7 +89,7 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
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const sectionState = state[name];
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_assertNotStringContainer(name, parameterType, sectionState);
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const stateDict = sectionState ?? {};
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const innerResult = walkNativeState(inputConnections, section.parameters, stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys });
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const innerResult = walkNativeState(inputConnections, section.parameters, stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
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if (Object.keys(innerResult).length > 0) {
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result[name] = innerResult;
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}
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@@ -1 +1 @@
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-
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+
{"version":3,"file":"walker.js","sourceRoot":"","sources":["../../src/workflow/walker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AASH,OAAO,EAAE,aAAa,EAAE,mBAAmB,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACxF,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAE7C,uEAAuE;AACvE,MAAM,CAAC,MAAM,UAAU,GAAkB,MAAM,CAAC,YAAY,CAAC,CAAC;AAyB9D;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,eAAe,CAC7B,gBAAyC,EACzC,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,OAA2B;IAE3B,MAAM,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC;IAC/B,MAAM,gBAAgB,GAAG,OAAO,EAAE,gBAAgB,IAAI,KAAK,CAAC;IAC5D,MAAM,mBAAmB,GAAG,OAAO,EAAE,mBAAmB,IAAI,KAAK,CAAC;IAClE,MAAM,YAAY,GAAG,OAAO,EAAE,YAAY,IAAI,KAAK,CAAC;IACpD,MAAM,MAAM,GAA4B,EAAE,CAAC;IAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IAEtC,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtB,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,8CAA8C;YAC9C,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAC3E,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,WAAW,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,SAAiC,CAAC;YACjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEhC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;YAE5D,iEAAiE;YACjE,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;gBAC3C,CAAC,CAAE,WAAyC;gBAC5C,CAAC,CAAC,EAAE,CAAC;YACP,IAAI,aAAqB,CAAC;YAC1B,IAAI,YAAY,EAAE,CAAC;gBACjB,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC;YAC/D,CAAC;iBAAM,CAAC;gBACN,MAAM,mBAAmB,GAAG,mBAAmB,CAAC,SAAS,EAAE,gBAAgB,CAAC,CAAC;gBAC7E,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,MAAM,EAAE,mBAAmB,CAAC,MAAM,CAAC,CAAC;YAC1E,CAAC;YAED,MAAM,SAAS,GAA8B,EAAE,CAAC;YAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE,CAAC;gBACvC,MAAM,aAAa,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1C,MAAM,cAAc,GAAG,GAAG,SAAS,IAAI,CAAC,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,eAAe,CACpC,gBAAgB,EAChB,MAAM,CAAC,UAAU,EACjB,aAAa,EACb,YAAY,EACZ,EAAE,MAAM,EAAE,cAAc,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAChF,CAAC;gBACF,SAAS,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YACjC,CAAC;YAED,8EAA8E;YAC9E,yEAAyE;YACzE,yEAAyE;YACzE,IAAI,YAAY,IAAI,IAAI,IAAI,KAAK,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC1D,MAAM,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,YAAY,EAAE,CAAC;YAC1C,MAAM,OAAO,GAAG,SAAkC,CAAC;YACnD,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEjC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC7D,MAAM,SAAS,GAAI,YAAwC,IAAI,EAAE,CAAC;YAElE,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,OAAO,CAAC,UAAU,EAClB,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAC3E,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,cAAc,GAAG,YAAY,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,CAAC,CAAC;YACjE,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC;YAChC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,gBAAgB,EAAE,CAAC;QACrB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,MAAM,IAAI,eAAe,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC;YACzC,CAAC;QACH,CAAC;IACH,CAAC;SAAM,IAAI,mBAAmB,EAAE,CAAC;QAC/B,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC1B,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC;YAC3B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,MAAe;IAEf,MAAM,MAAM,GAA4B,EAAE,CAAC;IAE3C,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,MAAM,WAAW,GAAG,gBAAgB,CAClC,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,SAAS,CACV,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,a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package/package.json
CHANGED
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{
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"name": "@galaxy-tool-util/schema",
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"version": "
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"version": "1.1.0",
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"description": "Effect Schema parameter types and validators for Galaxy tools",
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"effect": "^3.21.0",
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36
36
|
"yaml": "^2.8.3"
|
|
37
37
|
},
|
|
38
|
-
"devDependencies": {
|
|
39
|
-
"@galaxy-tool-util/core": "0.3.0"
|
|
40
|
-
},
|
|
38
|
+
"devDependencies": {},
|
|
41
39
|
"scripts": {
|
|
42
40
|
"build": "tsc && node ../../scripts/copy-schema-assets.mjs",
|
|
43
41
|
"typecheck": "tsc --noEmit",
|