Individual skill
tooluniverse-lab-data-standardization
Convert lab instrument output files (CSV, TSV, Excel, PDF — plate readers, spectrophotometers like NanoDrop, qPCR instruments, cell counters, chromatography systems) into a standardized Allotrope-Simple-Model-inspired JSON document plus a flattened 2D CSV, for LIMS/ELN upload or downstream analysis. Use when someone asks to "convert this instrument file", "standardize this lab data", "prepare this for LIMS upload", "what format is this plate reader/NanoDrop/qPCR output in", "turn this CSV into ASM/Allotrope format", or "separate the raw and calculated values in this instrument export". NOT for general data wrangling of arbitrary tabular data unrelated to lab instruments (use tooluniverse-data-wrangling), NOT for genomics/proteomics-specific file formats like FASTQ/VCF/mzML (use tooluniverse-fastq-qc, tooluniverse-variant-analysis, or tooluniverse-proteomics-analysis). Honest: never fabricates a measurement value; if a vendor's native parser (allotropy) is unavailable it says so and...
plugins/tooluniverse/skills/tooluniverse-lab-data-standardization/SKILL.md
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- Apache-2.0
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SKILL.mdcore · 6,716 bytesSKILL.mdcore · 6,716 bytesSKILL.mdcore · 6,716 bytesSKILL.mdcore · 6,716 bytesSKILL.mdcore · 6,716 bytesreferences/field_classification_guide.mddoc · 2,774 bytesreferences/schema_overview.mddoc · 2,695 bytesreferences/supported_instruments.mddoc · 2,555 bytesscripts/convert_instrument_data.pyruns · 14,410 bytesscripts/flatten_to_csv.pyruns · 1,703 bytesscripts/validate_output.pyruns · 4,800 bytes
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# Lab Instrument Data Standardization
Convert raw instrument output into a standardized, structured format —
distinguishing raw measurements from calculated/derived values with
explicit traceability — for LIMS/ELN upload, data lakes, or downstream
analysis.
## Honesty contract (read first)
1. **Never fabricate a value.** Every number in the output JSON/CSV must
come directly from the source file. If a value can't be found or
confidently parsed, it is omitted — never guessed.
2. **Never claim certified ASM output you didn't produce.** Tier 1 (native
`allotropy` parsing) produces genuine Allotrope Simple Model documents.