application: showfeat [
  documentation: "Display features of a sequence in pretty format"
  groups: "Display, Feature tables"
    relations: "EDAM:0000160 topic Sequence features"
    relations: "EDAM:0000092 topic Data rendering and visualisation"
    relations: "EDAM:0000564 operation Sequence rendering"
]

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

  seqall: sequence [
    parameter: "Y"
    type: "any"
    features: "Y"
    relations: "EDAM:0000849 data Sequence record"
  ]

endsection: input

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

  string: sourcematch [
    additional: "Y"
    default: "*"
    information: "Source of feature to display"
    help: "By default any feature source in the feature table is
           shown. You can set this to match any feature source you wish to
           show. \
           The source name is usually either the name of the program that
           detected the feature or it is the feature table (eg: EMBL) that
           the feature came from. \
           The source may be wildcarded by using '*'. \
           If you wish to show more than one source, separate their names
           with the character '|', eg: \
           gene* | embl"
    knowntype: "feature source list"
    relations: "EDAM:0000856 data Sequence feature source"
  ]

  string: typematch [
    additional: "Y"
    default: "*"
    information: "Type of feature to display"
    help: "By default any feature type in the feature table is shown.
           You can set this to match any feature type you wish to show. \
           See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL
           feature types and see Appendix A of the Swissprot user manual in
           http://www.expasy.org/sprot/userman.html for a list of the Swissprot
           feature types. \
           The type may be wildcarded by using '*'. \
           If you wish to show more than one type, separate their names with
           the character '|', eg: \
           *UTR | intron"
    knowntype: "feature key list"
    relations: "EDAM:0001020 data Sequence feature key"
  ]

  string: tagmatch [
    additional: "Y"
    default: "*"
    information: "Tag of feature to display"
    help: "Tags are the types of extra values that a feature may have.
           For example in the EMBL feature table, a 'CDS' type of feature
           may have the tags '/codon', '/codon_start', '/db_xref',
           '/EC_number', '/evidence', '/exception', '/function', '/gene',
           '/label', '/map', '/note', '/number', '/partial', '/product',
           '/protein_id', '/pseudo', '/standard_name', '/translation',
           '/transl_except', '/transl_table', or '/usedin'. Some of these
           tags also have values, for example '/gene' can have the value of
           the gene name. \
           By default any feature tag in the feature table is shown. You can
           set this to match any feature tag you wish to show. \
           The tag may be wildcarded by using '*'. \
           If you wish to show more than one tag, separate their names with
           the character '|', eg: \
           gene | label"
    knowntype: "feature tag list"
    relations: "EDAM:0001021 data Sequence feature qualifier"
  ]

  string: valuematch [
    additional: "Y"
    default: "*"
    information: "Value of feature tags to display"
    help: "Tag values are the values associated with a feature tag.
           Tags are the types of extra values that a feature may have. For
           example in the EMBL feature table, a 'CDS' type of feature may
           have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
           '/evidence', '/exception', '/function', '/gene', '/label', '/map',
           '/note', '/number', '/partial', '/product', '/protein_id',
           '/pseudo', '/standard_name', '/translation', '/transl_except',
           '/transl_table', or '/usedin'. Only some of these tags can have
           values, for example '/gene' can have the value of the gene name.
           By default any feature tag value in the feature table is shown.
           You can set this to match any feature tag value you wish to show. \
           The tag value may be wildcarded by using '*'. \
           If you wish to show more than one tag value, separate their names
           with the character '|', eg: \
           pax* | 10"
    knowntype: "feature tagvalue list"
    relations: "EDAM:0001021 data Sequence feature qualifier"
  ]

  list: sort [
    additional: "Y"
    default: "start"
    minimum: "1"
    maximum: "1"
    header: "Sorting features"
    values: "source:Sort by Source, start:Sort by Start position,
             type:Sort by Type, nosort:No sorting done"
    delimiter: ","
    codedelimiter: ":"
    information: "Sort features by Type, Start or Source,
                  Nosort (don't sort - use input order) or join coding
                  regions together and leave other features in the input
                  order"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: joinfeatures [
    additional: "Y"
    default: "N"
    information: "Join coding regions together"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]
 
  range: annotation [
    additional: "Y"
    default: ""
    information: "Regions to mark (eg: 4-57 promoter region
                  78-94 first exon)"
    help: "Regions to annotate by marking. \
           If this is left blank, then no annotation is added. \
           A set of regions is specified by a set of pairs of positions
           followed by optional text. \
           The positions are integers. \
           They are followed by any text (but not digits when on the
           command-line). \
           Examples of region specifications are: \
           24-45 new domain 56-78 match to Mouse \
           1-100 First part 120-156 oligo \
           A file of ranges to annotate (one range per line) can be specified
           as '@filename'."
    expected: "If this is left blank, then no annotation is
               added."
    relations: "EDAM:0001017 data Sequence range"
  ]

endsection: additional

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

  boolean: html [
    default: "N"
    information: "Use HTML formatting"
    outputmodifier: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: id [
    default: "Y"
    information: "Show sequence ID"
    help: "Set this to be false if you do not wish to display the ID
           name of the sequence."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: description [
    default: "Y"
    information: "Show description"
    help: "Set this to be false if you do not wish to display the
           description of the sequence."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: scale [
    default: "Y"
    information: "Show scale line"
    help: "Set this to be false if you do not wish to display the
           scale line."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  integer: width [
    default: "60"
    minimum: "0"
    information: "Width of graphics lines"
    help: "You can expand (or contract) the width of the
           ASCII-character graphics display of the positions of the features
           using this value. \
           For example, a width of 80 characters would cover a standard page
           width and a width a 10 characters would be nearly unreadable. \
           If the width is set to less than 4, the graphics lines and the
           scale line will not be displayed."
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: collapse [
    default: "N"
    information: "Display features with the same type on one
                  line"
    help: "If this is set, then features from the same source and of
           the same type and sense are all printed on the same line. For
           instance if there are several features from the EMBL feature table
           (ie. the same source) which are all of type 'exon' in the same
           sense, then they will all be displayed on the same line. This
           makes it hard to distinguish overlapping features. \
           If this is set to false then each feature is displayed on a
           separate line making it easier to distinguish where features start
           and end."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: forward [
    default: "Y"
    information: "Display forward sense features"
    help: "Set this to be false if you do not wish to display forward
           sense features."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: reverse [
    default: "Y"
    information: "Display reverse sense features"
    help: "Set this to be false if you do not wish to display reverse
           sense features."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: unknown [
    default: "Y"
    information: "Display unknown sense features"
    help: "Set this to be false if you do not wish to display unknown
           sense features. (ie. features with no directionality - all protein
           features are of this type and some nucleic features (for example,
           CG-rich regions))."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: strand [
    default: "N"
    information: "Display strand of features"
    help: "Set this if you wish to display the strand of the features.
           Protein features are always directionless (indicated by '0'),
           forward is indicated by '+' and reverse is '-'."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: origin [
    default: "N"
    information: "Display source of features"
    help: "Set this if you wish to display the origin of the features.
           \
           The source name is usually either the name of the program that
           detected the feature or it is the name of the feature table (eg:
           EMBL) that the feature came from."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: position [
    default: "N"
    information: "Display position of features"
    help: "Set this if you wish to display the start and end position
           of the features. If several features are being displayed on the
           same line, then the start and end positions will be joined by a
           comma, for example: '189-189,225-225'."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: type [
    default: "Y"
    information: "Display type of features"
    help: "Set this to be false if you do not wish to display the type
           of the features."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: tags [
    default: "N"
    information: "Display tags of features"
    help: "Set this to be false if you do not wish to display the tags
           and values of the features."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: values [
    default: "Y"
    information: "Display tag values of features"
    help: "Set this to be false if you do not wish to display the tag
           values of the features. If this is set to be false, only the tag
           names will be displayed. If the tags are not displayed, then the
           values will not be displayed. The value of the 'translation' tag
           is never displayed as it is often extremely long."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: stricttags [
    default: "N"
    information: "Only display the matching tags"
    help: "By default if any tag/value pair in a feature matches the
           specified tag and value, then all the tags/value pairs of that
           feature will be displayed. If this is set to be true, then only
           those tag/value pairs in a feature that match the specified tag
           and value will be displayed."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: advanced

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

  outfile: outfile [
    parameter: "Y"
    extension: "showfeat"
    knowntype: "showfeat output"
    relations: "EDAM:0001275 data General sequence features"
  ]

endsection: output