application: libgen [
  documentation: "Generate discriminating elements from
                  alignments."
  groups: "Protein:3D Structure"
  gui: "yes"
  batch: "yes"
  cpu: "medium"
  embassy: "signature"
  external: "hmmbuild HMMER 2.3.2"
  external: "blastpgp NCBI toolkit or blast executables"
  external: "modelfromalign SAM-tools http://compbio.soe.ucsc.edu/sam.html"
]

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

  dirlist: dafinpath [
    parameter: "Y"
    information: "Domain alignment directories"
    help: "This option specifies the location of DAF files (domain
           alignment files) (input). A 'domain alignment file' contains a
           sequence alignment of domains belonging to the same SCOP or CATH
           family. The file is in clustal format annotated with domain family
           classification information. The files generated by using
           SCOPALIGN will contain a structure-based sequence alignment of
           domains of known structure only. Such alignments can be extended
           with sequence relatives (of unknown structure) by using SEQALIGN."
    default: "./"
    extension: "daf"
    knowntype: "domain alignment"
    relations:  "EDAM: EMBASSY domain alignment file"                  
  ]

  matrixf: matrixfile [
    standard: "Y"
    information: "Residue substitution matrix."
    default: "EBLOSUM62"
    help: "This option specifies the residue substitution matrix.
           Epprofile for Gribskov profiles or EBLOSUM62 otherwise."
    expected: "Epprofile for Gribskov type, or EBLOSUM62"
    relations: "EDAM: Float comparison matrix"                             
  ]

endsection: input

section: required [
  information: "Required section"
  type: "page"
]

  list: mode [
    standard: "Y"
    default: "1"
    minimum: "1"
    maximum: "1"
    values: "1: Simple frequency matrix, 2: Gribskov profile, 3:
             Henikoff profile, 4: Hidden Markov model (HMMER), 5: Hidden
             Markov model (SAM-T2K), 6: Position-specific scoring matrix"
    delimiter: ","
    codedelimiter: ":"
    header: "Discrimininator type"
    information: "Select type."
    help: "This option specifies the mode of LIBGEN operation. LIBGEN
           generates one of six types of profile for each alignment.
           Supported profiles include simple frequency matrices, Gribskov
           profiles, Hennikoff profiles, hidden Markov models (HMMER
           package), hidden Markov models (SAM-T2K package) and
           position-specific scoring matrices."
    button: "Y"
    relations: "EDAM: Generic string array"                                
  ]

  integer: threshold [
    standard: "@($(mode)==1)"
    default: "75"
    minimum: "1"
    maximum: "100"
    information: "Enter threshold reporting percentage."
    help: "This option specifies the threshold reporting percentage.
           The threshold reporting percentage is used in the construction of
           the simple frequency matrix."
    relations: "EDAM: Generic integer"                                     
  ]

  float: gapopen [
    standard: "@($(mode)==1)"
    information: "Gap insertion penalty."
    default: "3.0"
    help: "This option specifies the gap insertion penalty. The gap
           insertion penalty is the score taken away when a gap is created.
           The best value depends on the choice of comparison matrix. The
           default value assumes you are using the EBLOSUM62 matrix for
           protein sequences, and the EDNAFULL matrix for nucleotide
           sequences."
    relations: "EDAM: Generic float"                                       
  ]

  float: gapextend [
    standard: "@($(mode)==1)"
    information: "Gap extension penalty."
    default: "0.3"
    help: "This option specifies the gap extension penalty. The gap
           extension, penalty is added to the standard gap penalty for each
           base or residue in the gap. This is how long gaps are penalized.
           Usually you will expect a few long gaps rather than many short
           gaps, so the gap extension penalty should be lower than the gap
           penalty."
    relations: "EDAM: Generic float"                                       
  ]

endsection: required

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

  outdir: outdir [
    parameter: "Y"
    default: "./"
    extension: "disc"
    information: "Discriminator file output directory"
    help: "This option specifies the location of discriminator files
           (output). The discriminator files contain one of the supported
           profiles, including simple frequency matrices, Gribskov profiles,
           Hennikoff profiles, hidden Markov models (HMMER package), hidden
           Markov models (SAM-T2K package) and position-specific scoring
           matrices."
    knowntype: "discriminator"
    relations:  "EDAM: Protein secondary database record"              
  ]

endsection: output
