application: xmltotext
[
  documentation: "Convert an XML document to a plain text format"
  groups: "Utils:Misc"
  gui: "yes"
  batch: "yes"
  cpu: "low"
  relations: "EDAM:0000220 topic File handling"
  relations: "EDAM:0000335 operation File reformatting"
]





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

infile: infile 
[
    parameter: "Y"
    knowntype: "ascii text"
    information: "ASCII text file"
    relations: "EDAM:0000969 data Text"
]

endsection: input





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

list: type
[
    standard: "Y"
    header: "File content"
    # Values are taken from EDAM "format" branch.  More could be added in time.
    values: "S:Sequence record, F:Sequence feature annotation, A:Sequence alignment"
    delimiter: ","
    codedelimiter: ":"
    information: "Enter the type of file content"
    help: "You must specify the type of file content so that appropriate output format options may be generated."
    relations: "EDAM:0002527 data Parameter or primitive"
]

list: seq
[
    standard: "@(type=='S')"
    # Must give sensible default
    default: "X"
    header: "Sequence format"
    # Values are taken from EDAM "format" branch and are sequence record formats supported by EMBOSS.  More could be added in time.
    # Must add list of formats.
    values: "X:XXX, X:XXX"
    delimiter: ","
    codedelimiter: ":"
    information: "Enter the ouput file format"
    help: "This option sets the format of a sequence output file."
    relations: "EDAM:0002129 identifier File format name"
]

list: feat
[
    standard: "@(type=='F')"
    # Must give sensible default
    default: "X"
    header: "Sequence feature format"
    # Values are taken from EDAM "format" branch and are sequence feature formats supported by EMBOSS.  More could be added in time.
    # Must add list of formats.
    values: "X:XXX, X:XXX"
    delimiter: ","
    codedelimiter: ":"
    information: "Enter the ouput file format"
    help: "This option sets the format of a sequence feature output file."
    relations: "EDAM:0002129 identifier File format name"
]

list: align
[
    standard: "@(type=='A')"
    # Must give sensible default
    default: "X"
    header: "Sequence alignment format"
    # Values are taken from EDAM "format" branch and are sequence alignment formats supported by EMBOSS.  More could be added in time.
    # Must add list of formats.
    values: "X:XXX, X:XXX"
    delimiter: ","
    codedelimiter: ":"
    information: "Enter the ouput file format"
    help: "This option sets the format of a sequence alignment output file."
    relations: "EDAM:0002129 identifier File format name"
]


endsection: required





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





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





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

outfile: outfile 
[
    parameter: "Y"
    knowntype: "ascii text"
    information: "ASCII text file"
    relations: "EDAM:0000969 data Text"
]

endsection: output