application: psiphi [
  documentation: "Calculates phi and psi torsion angles from
                  protein coordinates"
  groups: "protein:3D structure"
    relations: "EDAM:0002814 topic Protein structure"
    relations: "EDAM:0000249 operation Torsion angle calculation"
]

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

  infile: infile [
    parameter: "Y"
    information: "Clean protein structure coordinates file"
    knowntype: "protein clean coordinates"
    relations: "EDAM:0001460 data Protein structure"
  ]

endsection: input

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

  integer: chainnumber [
    standard: "Y"
    information: "Number of the chain for which torsion angles
                  should be calculated"
    default: "1"
    minimum: "1"
    relations: "EDAM:0001008 identifier Polypeptide chain ID"
  ]

  integer: startresiduenumber [
    standard: "Y"
    information: "First residue in chain for which torsion
                  angles should be calculated"
    default: "1"
    minimum: "1"
    relations: "EDAM:0001016 data Sequence position"
  ]

  integer: finishresiduenumber [
    standard: "Y"
    information: "Last residue in chain for which torsion
                  angles should be calculated (1 = last residue)"
    default: "1"
    relations: "EDAM:0001016 data Sequence position"
  ]

endsection: required

section: advanced [
  information: "Advanced section"
  type: "page"
]

endsection: advanced

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

  report: outfile [
    parameter: "Y"
    rformat: "table"
    multiple: "N"
    precision: "1"
    taglist: "float:phi float:psi"
    relations: "EDAM:0001544 data Ramachandran plot"
  ]

endsection: output