---
#' Annotations related parameters.
annotations:
  #' Thresholds related parameters.
  thresholds:
    #' MS2 annotation related parameters.
    ms2:
      #' For similarity.
      similarity:
        #' For edges. FLOAT
        edges: 0.7

#' Files.
files:
  #' Networks files.
  networks:
    #' Spectral networks files.
    spectral:
      #' Edges files.
      edges:
        #' Raw edges file.
        raw:
          #' Raw spectral edges file. STRING
          spectral: data/interim/features/example_edgesSpectra.tsv

  #' 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

  #' 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

#' Names of the different variables in the input files.
names:
  #' Name of "source IDs" variable in the input. STRING
  source: CLUSTERID1

  #' Name of "target IDs" variable in the input. STRING
  target: CLUSTERID2
