appl: diffseq [
  documentation: "Find differences (SNPs) between nearly identical sequences"
  groups: "Alignment:Differences"
  gui: yes
  batch: yes
  cpu: medium
]

section: input [ info: "input Section" type: page ]
sequence: asequence  [
  parameter: "Y"
  type: "any"
  features: "Y"
]

sequence: bsequence  [
  parameter: "Y"
  type: "@($(asequence.protein) ? protein : nucleotide)"
  features: "Y"
]

endsection: input

section: required [ info: "required Section" type: page ]
integer: wordsize  [
  required: "Y"
  default: "10"
  minimum: "2"
  information: "Word size"
]

endsection: required

section: output [ info: "output Section" type: page ]
report: outfile  [
  required: "Y"
  rformat: "diffseq"
  information: "Output report file"
  taglist: "int:start int:end int:length str:name str:sequence str:first_feature str:second_feature"
]

featout: afeatout  [
  optional: "Y"
  default: "$(asequence.name).diffgff"
  information: "Feature file for output asequence"
  help: "File for output of first sequence's normal tab delimited gff's"
]

featout: bfeatout  [
  optional: "Y"
  default: "$(bsequence.name).diffgff"
  information: "Feature file for output bsequence"
  help: "File for output of second sequence's normal tab delimited gff's"
]

bool: columns  [
  optional: "Y"
  default: "N"
  information: "Output in columns format"
  help: "The default format for the output report file is to have several lines per difference giving the sequence positions, sequences and features. \ If this option is set true then the output report file's format is changed to a set of columns and no feature information is given."
]

endsection: output

