application: showalign [
  documentation: "Display a multiple sequence alignment in pretty format"
  groups: "Alignment:Multiple, Data retrieval:Sequence data"
    relations: "EDAM:0000182 topic Sequence alignment"
    relations: "EDAM:0000090 topic Data retrieval"
    relations: "EDAM:0000257 operation Data retrieval (sequence alignment)"
    relations: "EDAM:0000564 operation Sequence rendering"
]

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

  seqset: sequence [
    parameter: "Y"
    type: "gapany"
    aligned: "Y"
    help: "The sequence alignment to be displayed."
    relations: "EDAM:0000863 data Sequence alignment"
  ]

  matrix: matrix [
    additional: "Y"
    information: "Similarity scoring 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:0000874 data Comparison matrix"
  ]

endsection: input

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

  string: refseq [
    additional: "Y"
    default: "0"
    information: "The number or the name of the reference
                  sequence"
    help: "If you give the number in the alignment or the name of a
           sequence, it will be taken to be the reference sequence. The
           reference sequence is always shown in full and is the one against
           which all the other sequences are compared. If this is set to 0
           then the consensus sequence will be used as the reference
           sequence. By default the consensus sequence is used as the
           reference sequence."
    knowntype: "sequence id input"
    relations: "EDAM:0001063 identifier Sequence identifier"
  ]

  boolean: bottom [
    additional: "Y"
    default: "Y"
    information: "Display the reference sequence at the bottom"
    help: "If this is true then the reference sequence is displayed at
           the bottom of the alignment instead of the top."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  list: show [
    additional: "Y"
    default: "N"
    minimum: "1"
    maximum: "1"
    header: "What to show"
    values: "A:All of the sequences, I:Identities between the
             sequences, N:Non-identities between the sequences,
             S:Similarities between the sequences, D:Dissimilarities between
             the sequences"
    delimiter: ","
    codedelimiter: ":"
    information: "What to show"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  list: order [
    additional: "Y"
    default: "I"
    minimum: "1"
    maximum: "1"
    header: "Output order of the sequences"
    values: "I:Input order - no change, A:Alphabetical order of the
             names, S:Similarity to the reference sequence"
    delimiter: ","
    codedelimiter: ":"
    information: "Output order of the sequences"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: similarcase [
    additional: "Y"
    default: "Y"
    information: "Show similar residues in lower-case"
    help: "If this is set True, then when -show is set to
           'Similarities' or 'Non-identities' and a residue is similar but
           not identical to the reference sequence residue, it will be
           changed to lower-case. If -show is set to 'All' then
           non-identical, non-similar residues will be changed to lower-case.
           If this is False then no change to the case of the residues is
           made on the basis of their similarity to the reference sequence."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: consensus [
    additional: "Y"
    default: "Y"
    information: "Display the consensus line"
    help: "If this is true then the consensus line is displayed."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: additional

section: advanced [
  information: "Advanced section"
  type: "page"
]

  range: uppercase [
    default: ""
    information: "Regions to put in uppercase (eg: 4-57,78-94)"
    help: "Regions to put in uppercase. \
           If this is left blank, then the sequence case is left alone. \
           A set of regions is specified by a set of pairs of positions. \
           The positions are integers. \
           They are separated by any non-digit, non-alpha character. \
           Examples of region specifications are: \
           24-45, 56-78 \
           1:45, 67=99;765..888 \
           1,5,8,10,23,45,57,99"
    expected: "If this is left blank, then the sequence case is
               left alone."
    relations: "EDAM:0001017 data Sequence range"
  ]

  boolean: number [
    default: "Y"
    information: "Number the sequences"
    help: "If this option is true then a line giving the positions in
           the alignment is displayed every 10 characters above the
           alignment."
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: ruler [
    default: "Y"
    information: "Display ruler"
    help: "If this option is true then a ruler line marking every 5th
           and 10th character in the alignment is displayed."
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  integer: width [
    default: "60"
    minimum: "1"
    information: "Width of sequence to display"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  integer: margin [
    default: "-1"
    minimum: "-1"
    information: "Length of margin for sequence names"
    help: "This sets the length of the left-hand margin for sequence
           names. If the margin is set at 0 then no margin and no names are
           displayed. If the margin is set to a value that is less than the
           length of a sequence name then the sequence name is displayed
           truncated to the length of the margin. If the margin is set to -1
           then the minimum margin width that will allow all the sequence
           names to be displayed in full plus a space at the end of the name
           will automatically be selected."
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: html [
    default: "N"
    information: "Use HTML formatting"
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  range: highlight [
    default: ""
    information: "Regions to colour in HTML (eg: 4-57 red 78-94
                  green)"
    help: "Regions to colour if formatting for HTML. \
           If this is left blank, then the sequence is left alone. \
           A set of regions is specified by a set of pairs of positions. \
           The positions are integers. \
           They are followed by any valid HTML font colour. \
           Examples of region specifications are: \
           24-45 blue 56-78 orange \
           1-100 green 120-156 red \
           A file of ranges to colour (one range per line) can be specified
           as '@filename'."
    relations: "EDAM:0001017 data Sequence range"
  ]

  float: plurality [
    default: "50.0"
    minimum: "0.0"
    maximum: "100.0"
    information: "Plurality check % for consensus"
    help: "Set a cut-off for the % of positive scoring matches below
           which there is no consensus. The default plurality is taken as 50%
           of the total weight of all the sequences in the alignment."
    relations: "EDAM:0002146 data Threshold"
  ]

  float: setcase [
    default: "@( $(sequence.totweight) / 2)"
    information: "Threshold above which the consensus is given
                  in uppercase"
    help: "Sets the threshold for the scores of the positive matches
           above which the consensus is in upper-case and below which the
           consensus is in lower-case. By default this is set to be half of
           the (weight-adjusted) number of sequences in the alignment."
    relations: "EDAM:0002146 data Threshold"
  ]

  float: identity [
    default: "0.0"
    minimum: "0.0"
    maximum: "100.0"
    information: "Required % of identities at a position for
                  consensus"
    help: "Provides the facility of setting the required number of
           identities at a position for it to give a consensus. Therefore, if
           this is set to 100% only columns of identities contribute to the
           consensus."
    relations: "EDAM:0002146 data Threshold"
  ]

  boolean: gaps [
    default: "Y"
    information: "Use gap characters in consensus"
    help: "If this option is true then gap characters can appear in
           the consensus. The alternative is 'N' for nucleotide, or 'X' for
           protein"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    knowntype: "showalign output"
    relations: "EDAM:0000863 data Sequence alignment"
  ]

endsection: output