---
#' Files.
files:
  #' Libraries files.
  libraries:
    #' Structure organism pairs libraries.
    sop:
      #' List of prepared structure organism pairs libraries.
      prepared:
        #' RT prepared structure organism pairs libraries. STRING
        rt: data/interim/libraries/sop/rt_prepared.tsv.gz

    #' Temporal libraries. STRING
    temporal:
      #' List of experimental temporal libraries.
      exp:
        #' List of experimental temporal libraries (CSV). STRING
        csv: [ ]

        #' List of experimental temporal libraries (MGF).
        mgf:
          #' List of negative experimental temporal libraries (MGF). STRING
          neg: [ ]

          #' List of positive experimental temporal libraries (MGF). STRING
          pos: [ ]

      #' List of in silico temporal libraries.
      is:
        #' List of in silico temporal libraries (CSV). STRING
        csv: [ ]

        #' List of in silico temporal libraries (MGF).
        mgf:
          #' List of negative in silico temporal libraries (MGF). STRING
          neg: [ ]

          #' List of positive in silico temporal libraries (MGF). STRING
          pos: [ ]

      #' List of prepared temporal libraries. STRING
      prepared:
        - data/interim/libraries/rt/prepared.tsv.gz

#' Names of the different variables in the input files.
names:
  #' Name of "InChIKey" variable in the input. STRING
  inchikey: inchikey

  #' Name of fields present in the MGF.
  mgf:
    #' Name of "InChIKey" in MGF. STRING
    inchikey: ~

    #' Name of "retention time" in MGF. STRING
    retention_time: RTINSECONDS

    #' Name of "SMILES" in MGF. STRING
    smiles: SMILES

  #' Name of "retention time" variable.
  rt: 
    #' Name of "retention time" variable in the library. STRING
    library: rt

  #' Name of "SMILES" variable in the input. STRING
  smiles: smiles

#' Units of the different variables in the input files.
units:
  #' Unit of the "retention time" variable in the input files.
  #' Must be "seconds" or "minutes". STRING
  rt: seconds
