fdrawtree.acd 6.69 KB
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application: fdrawtree [
  documentation: "Plots an unrooted tree diagram"
  groups: "Phylogeny:Tree drawing"
  batch: "no"
  embassy: "phylipnew"
  relations:  "EDAM_topic:0084 Phylogenetics"
  relations:  "EDAM_topic:0092 Data visualisation"
  relations:  "EDAM_operation:0567 Phylogenetic tree rendering"
]

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

  string: fontfile [
    default: "font1"
    information: "Fontfile name"
    knowntype: "phylip font"
    relations:  "EDAM_identifier:1050 File name"
  ]

  tree: intreefile [
    parameter: "Y"
    knowntype: "newick"
    information: "Phylip tree file"
    relations:  "EDAM_data:0872 Phylogenetic tree"
  ]

endsection: input

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

endsection: additional

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

  outfile: plotfile [
    parameter: "Y"
    knowntype: "drawtree output"
    information: "Phylip drawtree output file"
    relations:  "EDAM_data:0872 Phylogenetic tree"
  ]

  list: plotter [
    additional: "Y"
    minimum: "1"
    maximum: "1"
    header: "Plotter or printer"
    values: "l:Postscript printer file format;
             m:PICT format (for drawing programs);
             j:HP Laserjet 75 dpi PCL file format;
             s:HP Laserjet 150 dpi PCL file format;
             y:HP Laserjet 300 dpi PCL file format;
             w:MS-Windows Bitmap;
             f:FIG 2.0 drawing program format;
             a:Idraw drawing program format;
             z:VRML Virtual Reality Markup Language file;
             n:PCX 640x350 file format (for drawing programs);
             p:PCX 800x600 file format (for drawing programs);
             q:PCX 1024x768 file format (for drawing programs);
             k:TeKtronix 4010 graphics terminal;
             x:X Bitmap format;
             v:POVRAY 3D rendering program file;
             r:Rayshade 3D rendering program file;
             h:Hewlett-Packard pen plotter (HPGL file format);
             d:DEC ReGIS graphics (VT240 terminal);
             e:Epson MX-80 dot-matrix printer;
             c:Prowriter/Imagewriter dot-matrix printer;
             t:Toshiba 24-pin dot-matrix printer;
             o:Okidata dot-matrix printer;
             b:Houston Instruments plotter;
             u:other (one you have inserted code for)"
    information: "Plotter or printer the tree will be drawn on"
    default: "l"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  list: previewer [
    additional: "Y"
    minimum: "1"
    maximum: "1"
    header: "Previewing device"
    values: "n:Will not be previewed; I i:MSDOS graphics screen
             m:Macintosh screens; x:X Windows display; w:MS Windows display;
             k:TeKtronix 4010 graphics terminal; d:DEC ReGIS graphics (VT240
             terminal); o:Other (one you have inserted code for)"
    information: "Previewing device"
    default: "x"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  list: iterate [
    additional: "Y"
    minimum: "1"
    maximum: "1"
    header: "Iterate to improve tree"
    values: "n:No; e:Equal-Daylight algorithm; b:n-Body algorithm"
    information: "Iterate to improve tree"
    default: "e"
    relations: "EDAM_data:2527 Parameter"
  ]

  boolean: lengths [
    additional: "Y"
    default: "N"
    information: "Use branch lengths from user trees"
    relations: "EDAM_data:2527 Parameter"
  ]

  list: labeldirection [
    additional: "Y"
    minimum: "1"
    maximum: "1"
    header: "Lable direction"
    values: "a:along; f:fixed; r:radial; m:middle"
    information: "Label direction"
    default: "m"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: treeangle [
    information: "Angle the tree is to be plotted"
    default: "90.0"
    minimum: "-360.0"
    maximum: "360.0"
    additional: "Y"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: arc [
    information: "Degrees the arc should occupy"
    default: "360"
    minimum: "0.0"
    maximum: "360.0"
    additional: "Y"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: labelrotation [
    additional: "@($(style)!=c)"
    information: "Angle of labels (0 degrees is horizontal for
                  a tree growing vertically)"
    default: "90.0"
    minimum: "0.0"
    maximum: "360.0"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  toggle: rescaled [
    additional: "Y"
    default: "Y"
    information: "Automatically rescale branch lengths"
    relations: "EDAM_data:2527 Parameter"
  ]

  float: bscale [
    additional: "@(!$(rescaled))"
    default: "1.0"
    information: "Centimeters per unit branch length"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: treedepth [
    additional: "Y"
    default: "0.53"
    information: "Depth of tree as fraction of its breadth"
    minimum: "0.1"
    maximum: "100.0"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: xmargin [
    additional: "@($(plotter)!=r)"
    default: "1.65"
    minimum: "0.1"
    information: "Horizontal margin (cm)"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: ymargin [
    additional: "@($(plotter)!=r)"
    default: "2.16"
    minimum: "0.1"
    information: "Vertical margin (cm)"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: xrayshade [
    additional: "@($(plotter)==r)"
    default: "1.65"
    minimum: "0.1"
    information: "Horizontal margin (pixels)"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: yrayshade [
    additional: "@($(plotter)==r)"
    default: "2.16"
    minimum: "0.1"
    information: "Vertical margin (pixels)"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: paperx [
    additional: "Y"
    default: "20.63750"
    information: "Paper width"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: papery [
    additional: "Y"
    default: "26.98750"
    information: "Paper height"
    minimum: "0.1"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: pagesheight [
    additional: "Y"
    default: "1"
    information: "Number of trees across height of page"
    minimum: "1"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: pageswidth [
    additional: "Y"
    default: "1"
    information: "Number of trees across width of page"
    minimum: "1"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: hpmargin [
    additional: "Y"
    default: "0.41275"
    information: "Horizontal overlap (cm)"
    minimum: "0.001"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

  float: vpmargin [
    additional: "Y"
    default: "0.53975"
    information: "Vertical overlap (cm)"
    minimum: "0.001"
    relations: "EDAM_data:2152 Rendering parameter"
  ]

endsection: output