application: prettyplot [
  documentation: "Draw a sequence alignment with pretty formatting"
  groups: "Alignment:Multiple, Display"
  relations: "EDAM_topic:0182 Sequence alignment"
  relations: "EDAM_topic:0092 Data visualisation"
  relations: "EDAM_operation:0562 Sequence alignment reformatting"
  relations: "EDAM_operation:0564 Sequence rendering"
]

section: input [
  information: "Input section"
  type: "page"
]

  seqset: sequences [
    parameter: "Y"
    type: "gapany"
    aligned: "Y"
    relations: "EDAM_data:0863 Sequence alignment"
  ]

  matrix: matrixfile [
    additional: "Y"
    information: "Matrix file"
    protein: "$(acdprotein)"
    help: "This is the scoring matrix file used when comparing
           sequences. By default it is the file 'EBLOSUM62' (for proteins) or
           the file 'EDNAFULL' (for nucleic sequences). These files are
           found in the 'data' directory of the EMBOSS installation."
    relations: "EDAM_data:0874 Comparison matrix"
  ]

endsection: input

section: additional [
  information: "Additional section"
  type: "page"
]

  integer: residuesperline [
    additional: "Y"
    default: "50"
    information: "Number of residues to be displayed on each
                  line"
    help: "The number of residues to be displayed on each line"
    relations: "EDAM_data:1249 Sequence length"
  ]

  integer: blocksperline [
    additional: "Y"
    minimum: "1"
    maximum: "$(residuesperline)"
    failrange: "N"
    trueminimum: "Y"
    information: "Blocks of residues on each line"
    default: "1"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: ccolours [
    additional: "Y"
    default: "Y"
    information: "Colour residues by their consensus value."
    relations: "EDAM_data:2527 Parameter"
  ]

  string: cidentity [
    additional: "Y"
    information: "Colour to display identical residues (RED)"
    default: "RED"
    knowntype: "plot colour"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  string: csimilarity [
    additional: "Y"
    information: "Colour to display similar residues (GREEN)"
    default: "GREEN"
    knowntype: "plot colour"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  string: cother [
    additional: "Y"
    information: "Colour to display other residues (BLACK)"
    default: "BLACK"
    knowntype: "plot colour"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  boolean: docolour [
    additional: "Y"
    information: "Colour residues by table oily, amide etc."
    default: "N"
    relations: "EDAM_data:2527 Parameter"
  ]

  string: shade [
    additional: "Y"
    information: "Shading"
    help: "Set to BPLW for normal shading \
           (black, pale, light, white) \
           so for pair = 1.5,1.0,0.5 and shade = BPLW \
           Residues score Colour \
           1.5 or over... BLACK (B) \
           1.0 to 1.5 ... BROWN (P) \
           0.5 to 1.0 ... WHEAT (L) \
           under 0.5 .... WHITE (W) \
           The only four letters allowed are BPLW, in any order."
    default: ""
    maxlength: "4"
    minlength: "0"
    knowntype: "plot shading"
    pattern: "^([BPLW]{4})?$"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  array: pair [
    additional: "Y"
    information: "Values to represent identical similar
                  related"
    default: "1.5,1.0,0.5"
    minimum: "0.0"
    size: "3"
    sumtest: "N"
    knowntype: "threshold identity similar related"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  integer: identity [
    additional: "Y"
    information: "Only match those which are identical in all
                  sequences."
    default: "0"
    minimum: "0"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  boolean: doboxes [
    additional: "Y"
    information: "Display prettyboxes"
    default: "Y"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: boxcol [
    additional: "Y"
    information: "Colour the background in the boxes"
    default: "N"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  string: boxuse [
    additional: "Y"
    information: "Colour to be used for background. (GREY)"
    default: "GREY"
    knowntype: "plot colour"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  boolean: name [
    additional: "Y"
    information: "Display the sequence names"
    default: "Y"
    relations: "EDAM_data:2527 Parameter"
  ]

  integer: maxnamelen [
    additional: "Y"
    information: "Margin size for the sequence name."
    default: "10"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  boolean: number [
    additional: "Y"
    information: "Display the residue number"
    default: "Y"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: listoptions [
    additional: "Y"
    information: "Display the date and options used"
    default: "Y"
    relations: "EDAM_data:2527 Parameter"
  ]

  float: ratio [
    additional: "Y"
    information: "Plurality ratio for a consensus match"
    default: "0.5"
    minimum: "0.0"
    maximum: "1.0"
    relations: "EDAM_data:2527 Parameter"
  ]

  section: consensussection [
    information: "Consensus section"
    type: "frame"
  ]

    boolean: consensus [
      additional: "Y"
      information: "Display the consensus"
      default: "N"
    relations: "EDAM_data:2527 Parameter"
    ]

    boolean: collision [
      additional: "Y"
      information: "Allow collisions in calculating consensus"
      default: "Y"
    relations: "EDAM_data:2527 Parameter"
    ]

    list: alternative [
      additional: "Y"
      information: "Use alternative collisions routine"
      values: "0:Normal collision check. (default); 1:Compares
               identical scores with the max score found. So if any other
               residue matches the identical score then a collision has
               occurred.; 2:If another residue has a greater than or equal to
               matching score and these do not match then a collision has
               occurred.; 3:Checks all those not in the current consensus.If
               any of these give a top score for matching or identical scores
               then a collision has occured."
      help: "Values are 0:Normal collision check. (default) \
             1:Compares identical scores with the max score found. So if any
             other residue matches the identical score then a collision has
             occurred. \
             2:If another residue has a greater than or equal to matching
             score and these do not match then a collision has occurred. \
             3:Checks all those not in the current consensus.If any of these
             give a top score for matching or identical scores then a
             collision has occured."
      default: "0"
      minimum: "1"
      maximum: "1"
    relations: "EDAM_data:2527 Parameter"
    ]

  endsection: consensussection

  integer: showscore [
    additional: "Y"
    information: "Print residue scores"
    default: "-1"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  boolean: portrait [
    additional: "Y"
    information: "Set page to Portrait"
    default: "N"
    relations: "EDAM_data:2527 Parameter"
  ]

endsection: additional

section: output [
  information: "Output section"
  type: "page"
]

  graph: graph [
    standard: "Y"
    gdesc: "Pretty plot"
    relations: "EDAM_data:1711 Sequence alignment image"
  ]

endsection: output
