---
#' Files.
files:
  #' Libraries files.
  libraries:
    #' Structure organism pairs libraries.
    sop:
      #' List of prepared structure organism pairs libraries.
      prepared:
        #' Closed prepared structure organism pairs library. STRING
        closed: data/interim/libraries/sop/closed_prepared.tsv.gz
        #' ECMDB prepared structure organism pairs library. STRING
        ecmdb: data/interim/libraries/sop/ecmdb_prepared.tsv.gz
        #' HMDB prepared structure organism pairs library. STRING
        hmdb: data/interim/libraries/sop/hmdb_prepared.tsv.gz
        #' Lotus prepared structure organism pairs library. STRING
        lotus: data/interim/libraries/sop/lotus_prepared.tsv.gz
        #' RT prepared structure organism pairs library. STRING
        rt: data/interim/libraries/sop/rt_prepared.tsv.gz
        #' Spectral prepared structure organism pairs library. STRING
        spectral: data/interim/libraries/sop/spectral_prepared.tsv.gz

      #' Merged structure organism pairs library.
      merged:
        #' Merged structure organism pairs library keys. STRING
        keys: data/interim/libraries/sop/merged/keys.tsv.gz

        #' Organisms libraries.
        organisms:
          #' Organisms names. STRING
          names: data/interim/libraries/sop/merged/organisms/names.tsv.gz

          #' Organisms taxonomies.
          taxonomies:
            #' OTT organisms taxonomy. STRING
            ott: data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz

        #' Structures libraries.
        structures:
          #' Structures stereo. STRING
          stereo: data/interim/libraries/sop/merged/structures/stereo.tsv.gz

          #' Structures metadata. STRING
          metadata: data/interim/libraries/sop/merged/structures/metadata.tsv.gz

          #' Structures names. STRING
          names: data/interim/libraries/sop/merged/structures/names.tsv.gz

          #' Structures taxonomies.
          taxonomies:
            #' Classyfire structures taxonomy. STRING
            cla: data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz

            #' NPClassifier structures taxonomy. STRING
            npc: data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz

#' Organisms related parameters.
organisms:
  #' Organisms filter related parameters.
  filter:
    #' Filter library to restrict it to a portion of organisms only. BOOLEAN
    mode: no

    #' Level at which the library will be filtered.
    #' Must be one of "domain", "phylum", "class", "order",
    #' "family", "tribe", "genus", "species", "varietas" . STRING
    level: phylum

    #' Value to be applied for filtering.
    #' "OR" can be used as "|".
    # Example: "Simaroubaceae|Gentianaceae". STRING
    value: Streptophyta
