Instrument Data to Allotrope Converter

Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams.

Note: This skill utilizes the Bio-Informatics Pack. Scripts and references are located in: src-tauri/resources/packs/bio-informatics-pack/allotrope-conversion/

Workflow Overview

1. Detect instrument type from file contents (auto-detect or user-specified)
2. Parse file using allotropy library (native) or flexible fallback parser
3. Generate outputs:
   • ASM JSON (full semantic structure)
   • Flattened CSV (2D tabular format)
   • Python parser code (for data engineer handoff)
4. Deliver files with summary and usage instructions

When Uncertain: If you're unsure how to map a field to ASM (e.g., is this raw data or calculated?), ask the user for clarification. Refer to the pack's references/field_classification_guide.md for guidance.