application: ehmmemit [
  documentation: "Generate sequences from a profile HMM."
  groups: "HMM"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
  embassy: "hmmernew"
  external: "hmmemit HMMER 2.3.2 available from http://hmmer.wustl.edu/"
]

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

  infile: hmmfile [
    parameter: "Y"
    knowntype: "hmm"
    information: "HMMER hidden markov model file"
    help: "File containing one or more HMMs."
    relations:  "EDAM: HMMER hidden Markov model"                      
  ]

endsection: input

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

  integer: seed [
    default: "0"
    minimum: "0"
    information: "Random seed"
    help: "Set the random seed to <n>, where <n> is a positive
           integer. The default is to use time() to generate a different seed
           for each run, which means that two different runs of hmmemit on
           the same HMM will give slightly different results. You can use
           this option to generate reproducible results."
    relations: "EDAM: Generic integer"                                     
  ]

endsection: advanced

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

  boolean: a [
    additional: "Y"
    default: "N"
    information: "Output in selex format"
    help: "Write the generated sequences in an aligned format (SELEX)
           rather than FASTA."
    relations: "EDAM: Generic boolean"                                     
  ]

  boolean: c [
    standard: "Y"
    default: "N"
    information: "Output consensus sequence"
    help: "Predict a single majority-rule consensus sequence instead
           of sampling sequences from the HMM's probability distribution.
           Highly conserved residues (p >= 0.9 for DNA, p >= 0.5 for protein)
           are shown in upper case; others are shown in lower case. Some
           insert states may become part of the majority rule consensus,
           because they are used in >= 50% of generated sequences; when this
           happens, insert-generated residues are simply shown as 'x'."
    relations: "EDAM: Generic boolean"                                     
  ]

  integer: nseq [
    standard: "@(!$(c))"
    default: "10"
    information: "Number of sequences to produce"
    help: "Generate <n> sequences. Default is 10."
    relations: "EDAM: Generic integer"                                     
  ]

  boolean: q [
    additional: "Y"
    default: "N"
    information: "Suppress output except sequences."
    help: "Quiet; suppress all output except for the sequences
           themselves. Useful for piping or directing the output."
    relations: "EDAM: Generic boolean"                                     
  ]

  outfile: o [
    parameter: "Y"
    knowntype: "hmmemit output"
    information: "HMMER hmmemit program output file"
    help: "File of synthetic sequences."
    relations:  "EDAM: HMMER synthetic sequences record"               
  ]

endsection: output
