Batch script execution and automation

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v1/skills/batch-script-execution-and-automation

Use when you have generated a peak table or feature list output file from an external peak-picking tool (MZmine, XCMS, MS-DIAL, or Compound Discoverer) in its native export format and need to ingest it into LipidMatch for lipid identification without manual column remapping or format conversion.From its SKILL.md

Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill batch-script-execution-and-automation

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SKILL.md

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batch-script-execution-and-automation

Summary

Execute batch files and conversion scripts to transform peak-picking software output into LipidMatch-compatible input format, automating the file-format handoff between external peak-picking tools (MZmine, XCMS, MS-DIAL, Compound Discoverer) and the LipidMatch analysis pipeline.

When to use

You have generated a peak table or feature list output file from an external peak-picking tool (MZmine, XCMS, MS-DIAL, or Compound Discoverer) in its native export format and need to ingest it into LipidMatch for lipid identification without manual column remapping or format conversion.

When NOT to use

Input is already in LipidMatch-native format or has been previously converted
Using Waters mass spectrometry instruments or file formats, which LipidMatch does not currently support
Peak-picking output is from a tool not in the supported list (MZmine, XCMS, MS-DIAL, Compound Discoverer)

Inputs

peak table or feature list output file from MZmine, XCMS, MS-DIAL, or Compound Discoverer in native export format

Outputs

LipidMatch-compatible input file with mapped columns (m/z, retention time, intensity)

How to apply

Obtain the peak table output file from your chosen peak-picking software in its native export format. Retrieve the LipidMatch batch file and associated conversion scripts from the GarrettLab-UF/LipidMatch GitHub repository. Execute the batch file or conversion script against your peak-picker output file, which will automatically transform the data into LipidMatch-compatible format while mapping all required columns (m/z, retention time, intensity). After execution, validate the converted file structure against the LipidMatch input schema by checking row count, column headers, and data types to confirm successful format translation before proceeding to lipid identification.

Related tools

LipidMatch (downstream analysis pipeline that accepts the converted peak-picking output for lipid identification via in-silico fragment matching) — https://github.com/GarrettLab-UF/LipidMatch
MZmine (upstream peak-picking tool generating feature lists that serve as input to the batch conversion process)
XCMS (upstream peak-picking tool generating feature lists that serve as input to the batch conversion process)
MS-DIAL (upstream peak-picking tool generating feature lists that serve as input to the batch conversion process)
Compound Discoverer (upstream peak-picking tool generating feature lists that serve as input to the batch conversion process)

Evaluation signals

Converted file row count matches the original peak table (no data loss during transformation)
All required columns (m/z, retention time, intensity) are present with correct headers in the output file
Data types of numeric columns (m/z, intensity values) are correctly preserved as numeric, not text
No NULL or missing values appear in mandatory columns after conversion
Converted file successfully loads into LipidMatch without schema validation errors on subsequent ingestion

Limitations

LipidMatch does not currently support Waters instrument file formats
Conversion scripts are tool-specific; output from peak-picking tools outside the supported list (MZmine, XCMS, MS-DIAL, Compound Discoverer) may require custom adaptation
Column mapping assumes standard export formats from peak-picking tools; non-standard or custom exports may fail without modification to conversion scripts

Evidence

[other] a batch file for MZmine processing is provided in the repository to facilitate this file-format handoff: "a batch file for MZmine processing is provided in the repository to facilitate this file-format handoff"
[other] Execute the batch file or conversion script to transform the peak-picker output into the LipidMatch-compatible input format, ensuring all required columns (m/z, retention time, intensity) are mapped correctly.: "Execute the batch file or conversion script to transform the peak-picker output into the LipidMatch-compatible input format, ensuring all required columns (m/z, retention time, intensity) are mapped"
[other] Validate the converted file structure against LipidMatch input schema (row count, column headers, data types) to confirm successful format translation: "Validate the converted file structure against LipidMatch input schema (row count, column headers, data types) to confirm successful format translation"
[readme] a batch file for lipidomics with MZmine processing, and LipidMatch software/scripts: "a batch file for lipidomics with MZmine processing, and LipidMatch software/scripts"
[readme] The software does not currently support Waters files: "The software does not currently support Waters files"

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.