---
#' Annotations related parameters.
annotations:
  #' Perform approximative matching without precursor matching? BOOLEAN
  ms2approx: no

  #' Thresholds related parameters.
  thresholds:
    #' MS2 annotation related parameters.
    ms2:
      #' For similarity.
      similarity:
        #' For annotation. FLOAT
        annotation: 0.0

#' Files.
files:
  #' Annotations files.
  annotations:
    #' Raw annotations files.
    raw:
      #' List of spectral matching results.
      spectral:
        #' Spectral spectral matching results. STRING
        spectral: data/interim/annotations/example_spectralMatches.tsv.gz

  #' Libraries files.
  libraries:
    #' Spectral libraries. STRING
    spectral:
      #' List of negative spectral libraries. STRING
      neg:
        - data/interim/libraries/spectra/exp/massbank_neg.rds
        - data/interim/libraries/spectra/is/lotus_neg.rds

      #' List of positive spectral libraries. STRING
      pos:
        - data/interim/libraries/spectra/exp/massbank_pos.rds
        - data/interim/libraries/spectra/is/lotus_pos.rds

  #' Spectral files. STRING
  spectral:
    #' Raw spectral file. STRING
    raw: data/source/example_spectra.mgf

#' MS related parameters.
ms:
  #' Thresholds related parameters.
  thresholds:
    #' MS2 related parameters.
    ms2:
      #' Intensity threshold for MS2. INTEGER
      intensity: 5

  #' Polarity used. Must be "pos" or "neg". STRING
  polarity: pos

  #' Tolerances.
  tolerances:
    #' For mass.
    mass:
      #' Relative in ppm.
      ppm:
        #' Relative mass tolerance for MS2 in ppm. FLOAT
        ms2: 10

      #' Absolute in Dalton.
      dalton:
        #' Absolute mass tolerance for MS2 in Dalton. FLOAT
        ms2: 0.01
