Align with current tool-spec: parameters + data, inputs.json

[mmaelicke]

Summary

tool-runner-js relies on an outdated tool-spec. It uses parameters.json with a flat structure, mixes file inputs into parameters as type: file, and has no data section. No tools use this format anymore. This issue tracks aligning with the current spec.

Current (Outdated) Behavior

• Input file: parameters.json (spec says input.json; ecosystem uses inputs.json)
• Structure: Flat {toolName: {param: value, ...}} – no separation of parameters and data
• ToolConfig: Only parameters; no data field
• File inputs: Handled via type: file in parameters (asset-like)
• Environment: PARAM_FILE=/in/parameters.json, RUN_TOOL

Current Spec (tool-specs)

• Input file: /in/input.json or /in/inputs.json
• Structure: {toolName: {parameters: {...}, data: {...}}} – parameters and data separated
• tool.yml: parameters block for config args; data block for input files (with extension, description)
• File inputs: Declared in data section; referenced by name in input file

Required Changes

1. Input filename: Write inputs.json (or support both; gorun and tool-runner use inputs.json)
2. ToolConfig: Add data field – List<string> | Dict<string, DataConfig> (name-only list or dict with extension, description)
3. Input structure: Produce {toolName: {parameters: {...}, data: {name: "/in/path"}}}
4. Parameter handling: Remove type: file special casing; file inputs belong in data
5. Spec parsing: Parse data from tool.yml (support both list and dict formats per input.md)
6. Parameter building: Split user input into parameters vs data; validate each against spec

Tasks Checklist

• Add DataConfig interface (path/extension/description as in spec)
• Extend ToolConfig with data field
• Update tool.yml parser to extract data section
• Change output to inputs.json with parameters and data keys
• Remove type: file handling from parameter.ts; map data inputs via data section
• Update environment / compatibility: PARAM_FILE can point to inputs.json for legacy containers (json2args accepts both)
• Test with current templates (Python, Node with data section)

Reference

• tool-specs input.md: https://tool-spec.github.io/tool-specs/input/
• tool-spec-go inputs.go: structure for InputFile, ToolInput
• tool-runner (Python): models.py, runner.py for reference implementation