drawtree.yaml

!mobyle/program
name: drawtree
title: drawtree
description: Plots an unrooted tree diagram
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        format: '"drawtree <drawtree.params"'
        argpos: 0
        name: drawtree
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        comment: Tree in Newick format.
        prompt: Tree File (intree)
        format: '"ln -s "+str( treefile ) + " intree && "'
        simple: true
        argpos: -10
        mandatory: true
        name: treefile
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/inputprogramparameter
        format: '"0\n"'
        argpos: -1
        paramfile: drawtree.params
        name: screen_type
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Drawtree options
        name: options
        children:
        - !mobyle/inputprogramparameter
            prompt: Which plotter or printer will the tree be drawn on
            format: ("" , "P\n" + str(value) + "\n")[ value is not None and value
                != vdef ]
            simple: true
            argpos: 2
            paramfile: drawtree.params
            mandatory: true
            name: plotter
            command: false
            type: !mobyle/stringtype
                default: L
                options:
                - {label: PostScript printer file format (L), value: L}
                - {label: PICT format (M), value: M}
                - {label: HP Laserjet PCL file format (J), value: J}
                - {label: MS-Windows Bitmap (W), value: W}
                - {label: TeKtronix 4010 graphics terminal (K), value: K}
                - {label: Hewlett-Packard pen plotter (H), value: H}
                - {label: DEC ReGIS graphics (D), value: D}
                - {label: Houston Instruments plotter (B), value: B}
                - {label: Epson MX-80 dot-matrix printer (E), value: E}
                - {label: Prowriter/Imagewriter dot-matrix printer (C), value: C}
                - {label: Okidata dot-matrix printer (O), value: O}
                - {label: Toshiba 24-pin dot-matrix printer (T), value: T}
                - {label: PCX file format (P), value: P}
                - {label: X Bitmap format (X), value: X}
                - {label: FIG 2.0 format (F), value: F}
                - {label: Idraw drawing program format (A), value: A}
                - {label: VRML Virtual Reality Markup Language file (Z), value: Z}
                - {label: POVRAY 3D rendering program file (V), value: V}
                - {label: Rayshade 3D rendering program file (R), value: R}
        - !mobyle/inputprogramparagraph
            prompt: Bitmap options
            name: bitmap_options
            precond:
                plotter:
                    '#in': [X, W]
            children:
            - !mobyle/inputprogramparameter
                prompt: X resolution (in pixels)
                format: str( value ) + "\n"
                argpos: 3
                paramfile: drawtree.params
                mandatory: true
                name: xres
                command: false
                type: !mobyle/integertype {default: 500}
            - !mobyle/inputprogramparameter
                prompt: Y resolution (in pixels)
                format: str( value ) + "\n"
                argpos: 4
                paramfile: drawtree.params
                mandatory: true
                name: xyres
                command: false
                type: !mobyle/integertype {default: 500}
        - !mobyle/inputprogramparagraph
            prompt: Laserjet options
            name: laserjet_options
            precond: {plotter: J}
            children:
            - !mobyle/inputprogramparameter
                prompt: Laserjet resolution
                format: str(value) + "\n"
                argpos: 3
                paramfile: drawtree.params
                mandatory: true
                name: laserjet_resolution
                command: false
                type: !mobyle/stringtype
                    default: '3'
                    options:
                    - {label: 75 DPI (1), value: '1'}
                    - {label: 150 DPI (2), value: '2'}
                    - {label: 300 DPI (3), value: '3'}
        - !mobyle/inputprogramparagraph
            prompt: Paintbrush options
            name: pcx_options
            precond: {plotter: P}
            children:
            - !mobyle/inputprogramparameter
                prompt: Paintbrush PCX resolution
                format: str(value) + "\n"
                argpos: 3
                paramfile: drawtree.params
                mandatory: true
                name: pcx_resolution
                command: false
                type: !mobyle/stringtype
                    default: '3'
                    options:
                    - {label: EGA 640 X 350 (1), value: '1'}
                    - {label: VGA 800 X 600 (2), value: '2'}
                    - {label: VGA 1024 X 768 (3), value: '3'}
        - !mobyle/inputprogramparagraph
            prompt: POVRAY options
            name: pov_options
            precond: {plotter: V}
            children:
            - !mobyle/inputprogramparameter
                format: '"Y\n"'
                argpos: 2000
                paramfile: drawtree.params
                name: pov_validate
                command: false
                hidden: true
                type: !mobyle/stringtype {}
        - !mobyle/inputprogramparagraph
            prompt: PostScript options
            name: ps_options
            precond: {plotter: L}
            children:
            - !mobyle/inputprogramparameter
                prompt: Font (F)
                format: ("", "F\n"+str(value)+"\n")[value is not None and value !=
                    vdef]
                argpos: 5
                paramfile: drawtree.params
                name: font
                command: false
                type: !mobyle/stringtype
                    default: Times-Roman
                    options:
                    - {label: Courier, value: Courier}
                    - {label: Helvetica, value: Helvetica}
                    - {label: Helvetica-Bold, value: Helvetica-Bold}
                    - {label: Helvetica-BoldOblique, value: Helvetica-BoldOblique}
                    - {label: Helvetica-Oblique, value: Helvetica-Oblique}
                    - {label: Hershey, value: Hershey}
                    - {label: Times, value: Times}
                    - {label: Times-Bold, value: Times-Bold}
                    - {label: Times-BoldItalic, value: Times-BoldItalic}
                    - {label: Times-Italic, value: Times-Italic}
                    - {label: Times-Roman, value: Times-Roman}
        - !mobyle/inputprogramparagraph
            prompt: VRML options
            name: vrml_options
            precond: {plotter: Z}
            children:
            - !mobyle/inputprogramparameter
                format: '"Y\n"'
                argpos: 2000
                paramfile: drawtree.params
                name: vrml_validate
                command: false
                hidden: true
                type: !mobyle/stringtype {}
        - !mobyle/inputprogramparagraph
            prompt: Rayshade options
            name: ray_options
            precond: {plotter: R}
            children:
            - !mobyle/inputprogramparameter
                format: '"Y\n"'
                argpos: 2000
                paramfile: drawtree.params
                name: ray_validate
                command: false
                hidden: true
                type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            format: '"V\nN\n"'
            argpos: 1
            paramfile: drawtree.params
            name: preview
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Use branch lengths (B)
            format: ("B\n" , "")[ value ]
            argpos: 5
            paramfile: drawtree.params
            name: branch_lengths
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Angle of labels (L)
            argpos: 5
            paramfile: drawtree.params
            name: angle
            command: false
            type: !mobyle/stringtype {default: M}
        - !mobyle/inputprogramparameter
            prompt: 'Fixed angle: Are the labels to be plotted vertically (90), horizontally
                (0), or downwards (-90)  (L)?'
            format: ( "" , "L\nF\n"+ str( value ) +"\n")[ value is not None and value
                != vdef ]
            argpos: 7
            paramfile: drawtree.params
            name: fixed_angle
            precond:
                '#or':
                - {angle: ''}
                - {angle: F}
            command: false
            type: !mobyle/floattype {default: 0.0}
        - !mobyle/inputprogramparameter
            prompt: Rotation of tree (in degrees from 360 to -360) (R)
            format: ("" , "R\n" +str( value ) +"\n" )[ value is not None and value
                != vdef]
            argpos: 5
            paramfile: drawtree.params
            name: rotation
            command: false
            type: !mobyle/floattype {default: 0.0}
        - !mobyle/inputprogramparameter
            prompt: Angle of arc for tree (in degrees from 0 to 360)  (A)
            format: ( "" , "A\n" + str( value ) +"\n" )[ value is not None and value
                != vdef]
            argpos: 5
            paramfile: drawtree.params
            name: arc
            command: false
            type: !mobyle/floattype {default: 0.0}
        - !mobyle/inputprogramparameter
            prompt: Iterate to improve tree (I)
            argpos: 5
            paramfile: drawtree.params
            name: iterate
            command: false
            type: !mobyle/stringtype {default: E}
        - !mobyle/inputprogramparameter
            comment: 'Default value: Automatically rescaled'
            prompt: Scale of branch length (S)
            format: ( "" , "S\n"+ str( value )+ "\n")[ value is not None ]
            argpos: 5
            paramfile: drawtree.params
            name: scale
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparameter
            prompt: Try to avoid label overlap (D)
            format: ( "" , "D\n" )[ value ]
            argpos: 5
            paramfile: drawtree.params
            name: label_overlap
            precond:
                iterate: {'#ne': N}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Horizontal margins (M)
            format: ("" , "M\n" + str( value ) + "\n" + str(vertical_margins ) + "\n")[
                value is not None and value != vdef ]
            argpos: 10
            paramfile: drawtree.params
            name: horizontal_margins
            command: false
            type: !mobyle/floattype {default: 1.73}
        - !mobyle/inputprogramparameter
            prompt: Vertical margins (M)
            format: '""'
            argpos: 9
            paramfile: drawtree.params
            name: vertical_margins
            command: false
            type: !mobyle/floattype {default: 2.24}
        - !mobyle/inputprogramparameter
            prompt: Relative character height (C)
            format: ("", "C\n" + str( value ) + "\n" )[ value is not None and value
                != vdef ]
            argpos: 5
            paramfile: drawtree.params
            name: character_height
            command: false
            type: !mobyle/floattype {default: 0.3333}
    - !mobyle/inputprogramparameter
        format: '"Y\n"'
        argpos: 1000
        paramfile: drawtree.params
        name: confirm
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Graphic tree file
        filenames: '"plotfile"'
        name: plotfile
        precond:
            plotter:
                '#nin': [L, M, W, X]
    - !mobyle/outputprogramparameter
        prompt: Graphic tree file ( postscript format )
        filenames: '"plotfile.ps"'
        argpos: 10
        name: psfile
        precond: {plotter: L}
    - !mobyle/outputprogramparameter
        prompt: Graphic tree file ( pict format )
        filenames: '"plotfile.pict"'
        argpos: 10
        name: pictfile
        precond: {plotter: M}
    - !mobyle/outputprogramparameter
        prompt: Graphic tree file ( xbm format )
        filenames: '"plotfile.xbm"'
        argpos: 10
        name: xbmfile
        precond: {plotter: X}
    - !mobyle/outputprogramparameter
        prompt: Graphic tree file ( bmp format )
        filenames: '"plotfile.bmp"'
        argpos: 10
        name: bmpfile
        precond: {plotter: W}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"drawtree.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"drawtree.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: 'DRAWTREE interactively plots an unrooted tree diagram, with many options

    including orientation of tree and branches, label sizes and angles, margin

    sizes.  Particularly if you can use your computer screen to

    preview the plot, you can very effectively adjust the details of the plotting

    to get just the kind of plot you want.'
operations: ['EDAM_operation:0567']
topics: ['EDAM_topics:0092', 'EDAM_topics:0084']
documentation_links: ['http://bioweb2.pasteur.fr/docs/phylip/doc/drawtree.html']
env: {}