application: jaspscan [
  documentation: "Scans DNA sequences for transcription
                  factors"
  groups: "Nucleic:Transcription"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "DNA"
  ]

  list: menu [
    standard: "Y"
    default: "C"
    minimum: "1"
    maximum: "1"
    values: "C:Core,F:Fam,P:Phylofacts,N:CNE,O:POLII,S:SPLICE"
    delimiter: ","
    codedelimiter: ":"
    header: "Jaspar matrix set"
    information: "Matrix set"
    button: "Y"
  ]


  string:  matrices [
    standard: "Y"
    default: "all"
    information: "Comma separated matrix list"
    help: "The name 'all' reads in all matrix files from the selected \
           JASPAR matrix set. You can specify individual matrices by giving \
           their names with commas between then, such as: \
           'ma0001,ma0015'. \
           The case of the names is not important. You can specify a file of \
           matrix names to read in by giving the name of the file holding the \
           matrix names with a '@' character in front of it, for example, \
           '@matrix.list'. \
           Blank lines and lines starting with a hash character or '!' are
           ignored and all other lines are concatenated together with a comma \
           character ',' and then treated as the list of enzymes to search \
           for. \
           An example of a file of matrix names is: \
           ! my matrices \
           ma0001, ma0002 \
           ! other matrices \
           ma0010 \
           ma0032 \
           ma0053"
    knowntype: "jaspar matrix id"
  ]


endsection: input

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

  float: threshold [
    standard: "Y"
    default: "80.0"
    information: "Threshold percentage"
    help: "If the matrix score is greater than or equal to this percentage \
             then a hit will be reported"
  ]

endsection: required

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


  string:  exclude [
    default: ""
    additional: "Y"
    information: "Comma separated matrix list for exclusion"
    help: "The names of any matrices to exclude from the 'matrices' \
           list. Matrices are specified in the same way as for the \
           selection list."
    knowntype: "jaspar matrix id"
  ]

  boolean: both [
    additional: "Y"
    default: "N"
    information: "Scan both strands"
    help: "If set then both the forward and reverse strands are searched"
  ]

endsection: additional

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

  report: outfile [
    parameter: "Y"
    rformat: "seqtable"
    multiple: "Y"
    taglist: "float:pc=Score_Percent
              str:id=ID str:name=Name str:species=Species str:class=Class
              str:supergroup=Supergroup str:pseq=Protein_Seq
              str:exp=Experiment str:pmid=Source_PMID float:info=Info_Content
              str:jaspar=Closest_Jaspar str:transfac=Closest_Transfac
              float:mcs=MCS_Score str:built=Built_From"
  ]

endsection: output
