Validate Input Data

Description

Standalone command to validate all input data before starting the TIMA pipeline. This helps catch issues early and avoid wasting time on library downloads and processing.

Usage

validate_inputs(
  features = NULL,
  spectra = NULL,
  metadata = NULL,
  sirius = NULL,
  filename_col = "filename",
  organism_col = "organism",
  feature_col = "feature_id"
)

Arguments

features	Character path to features CSV/TSV file
spectra	Character path to MGF spectra file
metadata	Character path to metadata file
sirius	Character path to SIRIUS output directory or ZIP file
filename_col	Character name of filename column (default: "filename")
organism_col	Character name of organism column (default: "organism")
feature_col	Character name of feature ID column (default: "feature_id")

Value

Invisible TRUE if all checks pass, stops with error otherwise

Examples

library("tima")

# Validate all inputs before starting pipeline
validate_inputs(
  features = "data/features.csv",
  spectra = "data/spectra.mgf",
  sirius = "data/sirius_output"
)

# Validate with metadata consistency check
validate_inputs(
  features = "data/features.csv",
  metadata = "data/metadata.tsv"
)