application: ehmmcalibrate [
  documentation: "Calibrate HMM search statistics"
  groups: "HMM"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
  embassy: "hmmernew"
  external: "hmmcalibrate HMMER 2.3.2 available from http://hmmer.wustl.edu/"
]

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

  infile: inhmmfile [
    parameter: "Y"
    information: "HMMER hidden markov model file"
    knowntype: "hmm"
    help: "File containing an HMM."
    relations:  "EDAM: HMMER hidden Markov model"                      
  ]

endsection: input

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

  integer: cpu [
    default: "0"
    minimum: "0"
    information: "Number of CPUs"
    help: "Sets the maximum number of CPUs that the program will run
           on. The default is to use all CPUs in the machine. Overrides the
           HMMER NCPU environment variable. Only affects threaded versions of
           HMMER (the default on most systems)."
    relations: "EDAM: Generic integer"                                     
  ]

  integer: fixed [
    default: "0"
    minimum: "0"
    information: "Length fix for random sequences"
    help: "Fix the length of the random sequences to <n>, where <n> is
           a positive (and reasonably sized) integer. The default is instead
           to generate sequences with a variety of different lengths,
           controlled by a Gaussian (normal) distribution."
    relations: "EDAM: Generic integer"                                     
  ]

  float: mean [
    default: "350.0"
    information: "Mean length of synthetic sequences"
    help: "Set the mean length of the synthetic sequences to <x>,
           where <x> is a positive real number. The default is 350."
    relations: "EDAM: Generic float"                                       
  ]

  integer: num [
    default: "5000"
    minimum: "0"
    information: "Number of synthetic sequences"
    help: "Set the number of synthetic sequences to <n>, where <n> is
           a positive integer. If <n> is less than about 1000, the ft to the
           EVD may fail. Higher numbers of <n> will give better determined
           EVD parameters. The default is 5000; it was empirically chosen as
           a tradeoff between accuracy and computation time."
    relations: "EDAM: Generic integer"                                     
  ]

  boolean: pvm [
    default: "N"
    information: "Run on parallel virtual machines"
    help: "Run on a Parallel Virtual Machine (PVM). The PVM must
           already be running. The client program hmmcalibrate-pvm must be
           installed on all the PVM nodes. Optional PVM support must have
           been compiled into HMMER."
    relations: "EDAM: Generic boolean"                                     
  ]

  float: sd [
    default: "350.0"
    minimum: "0"
    information: "Standard deviation of syntheic sequences"
    help: "Set the standard deviation of the synthetic sequence length
           distribution to <x>, where <x> is a positive real number. The
           default is 350. Note that the Gaussian is left-truncated so that
           no sequences have lengths <= 0."
    relations: "EDAM: Generic float"                                       
  ]

  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 hmmcalibrate
           on the same HMM will give slightly different results. You can use
           this option to generate reproducible results for different
           hmmcalibrate runs on the same HMM."
    relations: "EDAM: Generic integer"                                     
  ]

endsection: advanced

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

  outfile: outhmmfile [
    parameter: "Y"
    information: "HMMER hmmcalibrate program output file"
    knowntype: "hmmcalibrate output"
    help: "File containing an HMM with EVD parameters."
    relations:  "EDAM: HMMER hidden Markov model"                      
  ]

  outfile: histfile [
    nullok: "Yes"
    nulldefault: "Yes"
    information: "HMMER histogram output file (optional)"
    knowntype: "hmmer histogram"
    help: "Save a histogram of the scores and the fitted theoretical
           curve to file."
    relations:  "EDAM: Histogram graph data"                           
  ]

endsection: output
