@galaxy-tool-util/cli 1.1.0 → 1.3.0

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Files changed (71) hide show
  1. package/dist/commands/annotate-connections.d.ts +30 -0
  2. package/dist/commands/annotate-connections.d.ts.map +1 -0
  3. package/dist/commands/annotate-connections.js +42 -0
  4. package/dist/commands/annotate-connections.js.map +1 -0
  5. package/dist/commands/connection-validation.d.ts +20 -0
  6. package/dist/commands/connection-validation.d.ts.map +1 -0
  7. package/dist/commands/connection-validation.js +26 -0
  8. package/dist/commands/connection-validation.js.map +1 -0
  9. package/dist/commands/cytoscapejs/_template-bundled.d.ts +2 -0
  10. package/dist/commands/cytoscapejs/_template-bundled.d.ts.map +1 -0
  11. package/dist/commands/cytoscapejs/_template-bundled.js +182 -0
  12. package/dist/commands/cytoscapejs/_template-bundled.js.map +1 -0
  13. package/dist/commands/cytoscapejs.d.ts +12 -0
  14. package/dist/commands/cytoscapejs.d.ts.map +1 -0
  15. package/dist/commands/cytoscapejs.js +62 -0
  16. package/dist/commands/cytoscapejs.js.map +1 -0
  17. package/dist/commands/mermaid.d.ts +2 -0
  18. package/dist/commands/mermaid.d.ts.map +1 -1
  19. package/dist/commands/mermaid.js +5 -1
  20. package/dist/commands/mermaid.js.map +1 -1
  21. package/dist/commands/summarize.d.ts +31 -0
  22. package/dist/commands/summarize.d.ts.map +1 -0
  23. package/dist/commands/summarize.js +85 -0
  24. package/dist/commands/summarize.js.map +1 -0
  25. package/dist/commands/validate-workflow.d.ts +1 -0
  26. package/dist/commands/validate-workflow.d.ts.map +1 -1
  27. package/dist/commands/validate-workflow.js +38 -3
  28. package/dist/commands/validate-workflow.js.map +1 -1
  29. package/dist/index.d.ts +3 -0
  30. package/dist/index.d.ts.map +1 -1
  31. package/dist/index.js +2 -0
  32. package/dist/index.js.map +1 -1
  33. package/dist/meta/extract-spec.d.ts +13 -0
  34. package/dist/meta/extract-spec.d.ts.map +1 -0
  35. package/dist/meta/extract-spec.js +90 -0
  36. package/dist/meta/extract-spec.js.map +1 -0
  37. package/dist/meta/index.d.ts +8 -0
  38. package/dist/meta/index.d.ts.map +1 -0
  39. package/dist/meta/index.js +21 -0
  40. package/dist/meta/index.js.map +1 -0
  41. package/dist/meta/spec-types.d.ts +40 -0
  42. package/dist/meta/spec-types.d.ts.map +1 -0
  43. package/dist/meta/spec-types.js +11 -0
  44. package/dist/meta/spec-types.js.map +1 -0
  45. package/dist/meta/specs.d.ts +4 -0
  46. package/dist/meta/specs.d.ts.map +1 -0
  47. package/dist/meta/specs.js +10 -0
  48. package/dist/meta/specs.js.map +1 -0
  49. package/dist/meta/types.d.ts +55 -0
  50. package/dist/meta/types.d.ts.map +1 -0
  51. package/dist/meta/types.js +9 -0
  52. package/dist/meta/types.js.map +1 -0
  53. package/dist/meta-build.d.ts +13 -0
  54. package/dist/meta-build.d.ts.map +1 -0
  55. package/dist/meta-build.js +60 -0
  56. package/dist/meta-build.js.map +1 -0
  57. package/dist/programs/galaxy-tool-cache.d.ts +5 -1
  58. package/dist/programs/galaxy-tool-cache.d.ts.map +1 -1
  59. package/dist/programs/galaxy-tool-cache.js +14 -56
  60. package/dist/programs/galaxy-tool-cache.js.map +1 -1
  61. package/dist/programs/gxwf.d.ts +7 -1
  62. package/dist/programs/gxwf.d.ts.map +1 -1
  63. package/dist/programs/gxwf.js +36 -184
  64. package/dist/programs/gxwf.js.map +1 -1
  65. package/dist/spec/build-program.d.ts +12 -0
  66. package/dist/spec/build-program.d.ts.map +1 -0
  67. package/dist/spec/build-program.js +102 -0
  68. package/dist/spec/build-program.js.map +1 -0
  69. package/package.json +10 -4
  70. package/spec/galaxy-tool-cache.json +177 -0
  71. package/spec/gxwf.json +693 -0
package/spec/galaxy-tool-cache.json ADDED
@@ -0,0 +1,177 @@
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+ {
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+ "name": "galaxy-tool-cache",
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+ "description": "Cache and inspect Galaxy tool metadata",
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+ "version": "1.0.0",
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+ "commands": [
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+ {
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+ "name": "add",
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+ "description": "Fetch a tool from ToolShed/Galaxy and cache it",
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+ "handler": "add",
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+ "args": [
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+ {
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+ "raw": "<tool_id>",
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+ "description": "Tool ID (full toolshed path or TRS ID)"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--version <ver>",
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+ "description": "Tool version"
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+ },
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ },
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+ {
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+ "flags": "--galaxy-url <url>",
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+ "description": "Galaxy instance URL for fallback"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "list",
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+ "description": "List cached tools",
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+ "handler": "list",
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+ "options": [
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+ {
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+ "flags": "--json",
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+ "description": "Output as JSON"
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+ },
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "info",
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+ "description": "Show metadata for a cached tool",
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+ "handler": "info",
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+ "args": [
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+ {
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+ "raw": "<tool_id>",
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+ "description": "Tool ID"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--version <ver>",
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+ "description": "Tool version"
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+ },
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "clear",
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+ "description": "Clear cached tools",
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+ "handler": "clear",
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+ "args": [
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+ {
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+ "raw": "[prefix]",
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+ "description": "Only clear tools matching this prefix"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "schema",
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+ "description": "Export JSON Schema for a cached tool's parameters",
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+ "handler": "schema",
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+ "args": [
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+ {
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+ "raw": "<tool_id>",
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+ "description": "Tool ID"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--version <ver>",
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+ "description": "Tool version"
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+ },
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+ {
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+ "flags": "--representation <rep>",
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+ "description": "State representation (e.g., workflow_step)",
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+ "default": "workflow_step"
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+ },
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+ {
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+ "flags": "--output <file>",
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+ "description": "Output file (default: stdout)"
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+ },
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "summarize",
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+ "description": "Emit a deterministic summary manifest for a cached Galaxy tool",
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+ "handler": "summarize",
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+ "args": [
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+ {
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+ "raw": "<tool_id>",
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+ "description": "Tool ID"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--version <ver>",
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+ "description": "Tool version"
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+ },
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+ {
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+ "flags": "--output <file>",
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+ "description": "Output file (default: stdout)"
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+ },
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "populate-workflow",
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+ "description": "Scan a workflow and cache all referenced tools",
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+ "handler": "populateWorkflow",
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+ "args": [
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+ {
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+ "raw": "<file>",
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+ "description": "Workflow file (.ga, .gxwf.yml)"
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+ }
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+ ],
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+ "options": [
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+ {
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+ "flags": "--cache-dir <dir>",
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+ "description": "Cache directory"
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+ },
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+ {
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+ "flags": "--galaxy-url <url>",
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+ "description": "Galaxy instance URL for fallback"
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+ }
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+ ]
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+ },
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+ {
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+ "name": "structural-schema",
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+ "description": "Export the structural JSON Schema for Galaxy workflows",
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+ "handler": "structuralSchema",
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+ "options": [
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+ {
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+ "flags": "--format <fmt>",
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+ "description": "Workflow format: format2 (default) or native",
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+ "default": "format2"
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+ },
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+ {
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+ "flags": "--output <file>",
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+ "description": "Output file (default: stdout)"
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+ }
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+ ]
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+ }
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+ ]
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+ }