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drawgram.yaml
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drawgram.yaml
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!mobyle/program
name: drawgram
title: drawgram
description: Plots a cladogram- or phenogram-like rooted tree
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
format: '"drawgram <drawgram.params"'
argpos: 0
name: drawgram
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: drawgram.params
name: screen_type
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Drawgram options
name: options
children:
- !mobyle/inputprogramparameter
prompt: Which plotter or printer will the tree be drawn on (P)
format: ("" , "P\n" + str(value) +"\n")[ value is not None and value !=
vdef ]
argpos: 2
paramfile: drawgram.params
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: xbitmap_options
precond:
plotter:
'#in': [X, W]
children:
- !mobyle/inputprogramparameter
prompt: X resolution (in pixels)
format: str( value ) + "\n"
argpos: 3
paramfile: drawgram.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: drawgram.params
mandatory: true
name: yres
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: drawgram.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: drawgram.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: 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: drawgram.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: POVRAY options
name: pov_options
precond: {plotter: V}
children:
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 2000
paramfile: drawgram.params
name: pov_validate
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: VRML options
name: vrml_options
precond: {plotter: Z}
children:
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 2000
paramfile: drawgram.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: drawgram.params
name: ray_validate
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"V\nN\n"'
argpos: 1
paramfile: drawgram.params
name: screen
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Tree grows... (H)
format: ( "" , "H\n" )[ value is not None and value != vdef ]
argpos: 5
paramfile: drawgram.params
name: grows
command: false
type: !mobyle/stringtype
default: Horizontally
options:
- {label: Vertically, value: Vertically}
- {label: Horizontally, value: Horizontally}
- !mobyle/inputprogramparameter
prompt: Tree style (S)
argpos: 5
paramfile: drawgram.params
name: tree_style
command: false
type: !mobyle/stringtype {default: C}
- !mobyle/inputprogramparameter
prompt: Use branch lengths (B)
format: ("B\n" , "")[ value ]
argpos: 5
paramfile: drawgram.params
name: branch_lengths
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: drawgram.params
name: horizontal_margins
command: false
type: !mobyle/floattype {default: 1.65}
- !mobyle/inputprogramparameter
prompt: Vertical margins
format: '""'
argpos: 9
paramfile: drawgram.params
name: vertical_margins
command: false
type: !mobyle/floattype {default: 2.16}
- !mobyle/inputprogramparameter
comment: 'Default value: Automatically rescaled'
prompt: Scale of branch length (R)
format: ("" , "R\n" +str( value ) +"\n")[ value is not None ]
argpos: 5
paramfile: drawgram.params
name: scale
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
prompt: Depth/Breadth of tree (D)
format: ( "" , "D\n" + str( value ) + "\n" )[ value is not None and value
!= vdef ]
argpos: 5
paramfile: drawgram.params
name: depth
command: false
type: !mobyle/floattype {default: 1.0}
- !mobyle/inputprogramparameter
comment: Enter the stem length as fraction of tree depth (a value between
0.0 and 1.0).
prompt: Stem-length/tree-depth (T)
format: ("" , "T\n" + str( value ) + "\n")[ value is not None and value
!= vdef ]
argpos: 5
paramfile: drawgram.params
name: stem
command: false
type: !mobyle/floattype {default: 0.05}
- !mobyle/inputprogramparameter
comment: Enter character height as fraction of tip spacing.
prompt: Character ht / tip space (C)
format: ("" , "C\n" + str( value ) +"\n")[ value is not None and value
!= vdef ]
argpos: 5
paramfile: drawgram.params
name: character_height
command: false
type: !mobyle/floattype {default: 0.3333}
- !mobyle/inputprogramparameter
prompt: Ancestral nodes (A)
format: ("" , "A\n" + str( value )+ "\n")[ value is not None and value
!= vdef ]
argpos: 5
paramfile: drawgram.params
name: ancestral
command: false
type: !mobyle/stringtype
default: I
options:
- {label: Intermediate (I), value: I}
- {label: Weighted (W), value: W}
- {label: Centered (C), value: C}
- {label: Inner (N), value: N}
- {label: So tree is V-shaped (V), value: V}
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 1000
paramfile: drawgram.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: '"drawgram.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"drawgram.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
comment: "DRAWGRAM interactively plots a cladogram- or\n\t phenogram-like rooted\
\ tree diagram, with many options including\n\t orientation of tree and branches,\
\ style of tree, label sizes and\n\t angles, tree depth, margin sizes, stem\
\ lengths, and placement of\n\t nodes in the tree. Particularly if you can \
\ use your computer to\n\t preview the plot, you can very effectively adjust\
\ the details of\n\t 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/drawgram.html']
env: {}