application: eiprscan [
  documentation: "Motif detection"
  groups: "Protein:Motifs"
  embassy: "iprscan"
]

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

  seqset: sequence [
    parameter: "Y"
    type: "gap"
    aligned: "N"
  ]

endsection: input

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

  list: appl [
    standard: "Y"
    default: "all"
    minimum: "1"
    maximum: "15"
    header: "Applications to use"
    values: "all:all, blastprodom:blastprodom, coils:coils,
             gene3d:gene3d, hmmpanther:hmmpanther, hmmpir:hmmpir,
	     hmmpfam:hmmpfam, hmmsmart:hmmsmart, hmmtigr:hmmtigr,
	     fprintscan:fprintscan, scanregexp:scanregexp,
	     profilescan:profilescan, superfamily:superfamily,
	     seq:seq, signalp:signalp, tmhmm:tmhmm"
    delimiter: ","
    codedelimiter: ":"
    information: "Application(s) to use"
  ]

  list: format [
    standard: "Y"
    default: "xml"
    minimum: "1"
    maximum: "1"
    header: "Output Formats"
    values: "raw:Raw, txt:Text, html:Html, xml:Xml, ebixml:EBIxml, gff:GFF"
    delimiter: ","
    codedelimiter: ":"
    information: "Format to use"
  ]

endsection: required

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

  string: email [
    additional: "Y"
    default: ""
    information: "Sumbitter email address"
    knowntype: "email input"
  ]

 
 list: trtable [
    additional: "Y"
    default: "0"
    minimum: "1"
    maximum: "1"
    header: "Genetic codes"
    values: "0:Standard; 1:Standard (with alternative initiation
             codons); 2:Vertebrate Mitochondrial; 3:Yeast Mitochondrial;
             4:Mold, Protozoan, Coelenterate Mitochondrial and
             Mycoplasma/Spiroplasma; 5:Invertebrate Mitochondrial; 6:Ciliate
             Macronuclear and Dasycladacean; 9:Echinoderm Mitochondrial;
             10:Euplotid Nuclear; 11:Bacterial; 12:Alternative Yeast Nuclear;
             13:Ascidian Mitochondrial; 14:Flatworm Mitochondrial;
             15:Blepharisma Macronuclear; 16:Chlorophycean Mitochondrial;
             21:Trematode Mitochondrial; 22:Scenedesmus obliquus;
             23:Thraustochytrium Mitochondrial"
    delimiter: ";"
    codedelimiter: ":"
    information: "Code to use"
    help: "Genetic codes used for translation"
  ]

  integer: trlen [
    default: "1"
    minimum: "1"
    information: "Minimum size of ORFs"
    help: "Minimum size of Open Reading Frames (ORFs) in
           the translations."
  ]

  boolean: iprlookup [
    additional: "Y"
    default: "N"
    information: "Turn on InterPro lookup for results"
  ]

  boolean: goterms [
    additional: "$(iprlookup)"
    default: "N"
    information: "Show GO terms is InterPro lookup is on"
  ]

  boolean: crc [
    additional: "Y"
    default: "Y"
    information: "Perform CRC64 check"
  ]

  boolean: altjobs [
    additional: "Y"
    default: "N"
    information: "Launch jobs alternatively (chunk after chunk)"
  ]


endsection: additional

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

  outfile: outfile [
    parameter: "Y"
    information: "EIPRSCAN program output file"
    knowntype: "eiprscan output"
  ]

endsection: output
