application: wordmatch [
  documentation: "Find regions of identity (exact matches) of two sequences"
  groups: "Alignment:Local"
    relations: "EDAM_topic:0182 Sequence alignment"
    relations: "EDAM_operation:0288 Sequence word comparison"
]

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

  seqset: asequence [
    parameter: "Y"
    aligned: "N"  
    type: "any"                                         
    relations: "EDAM_data:0849 Sequence record"
  ]

  seqall: bsequence [
    parameter: "Y"
    type: "@($(acdprotein) ? stopprotein : nucleotide)"
    relations: "EDAM_data:0849 Sequence record"
  ]

endsection: input

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

  integer: wordsize [
    standard: "Y"
    default: "4"
    minimum: "2"
    information: "Word size"
    relations: "EDAM_data:1250 Word size"
  ]

endsection: required

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

  toggle: dumpalign [
    default: "Y"
    additional: "Y"
    information: "Dump matches as alignments"
    relations: "EDAM_data:2527 Parameter"
  ]
  
  align: outfile [
    parameter: "Y"
    nullok: "@(!$(dumpalign))"
    aformat: "match"
    minseqs: "2"
    relations: "EDAM_data:1381 Sequence alignment (pair)"
  ]
 
  outfile: logfile [
    additional: "Y"
    default: "wordmatch.log"
    knowntype: "wordmatch log"
    information: "Wordmatch log output file"
    help: "Statistics on distribution of kmers and matches"
    relations: "EDAM_data:1678 Tool log"
  ]
  
  toggle: dumpfeat [
    default: "Y"
    additional: "Y"
    information: "Dump matches as feature files"
    relations: "EDAM_data:2527 Parameter"
  ]

  featout: aoutfeat [
    parameter: "Y"
    nullok: "@(!$(dumpfeat))"
    ofname: "$(asequence.name)"
    offormat: "gff"
    relations: "EDAM_data:1255 Feature record"
  ]

  featout: boutfeat [
    parameter: "Y"
    ofname: "$(bsequence.name)"
    offormat: "gff"
    nullok: "@(!$(dumpfeat))"
    relations: "EDAM_data:1255 Feature record"
  ]
 
endsection: output
