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boxshade_3.31.yaml
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628 lines (628 loc) · 25.2 KB
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!mobyle/program
name: boxshade
version: '3.31'
title: BOXSHADE
description: printouts from multiple-aligned protein or DNA sequences
authors: Hofmann, Baron
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
format: '"boxshade <boxshade.params"'
argpos: 0
name: boxshade
command: true
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Alignment File
format: str(value) + "\n"
simple: true
argpos: 1
paramfile: boxshade.params
mandatory: true
name: alignment
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1982']
data_terms: ['EDAM_data:0863']
- !mobyle/inputprogramparameter
format: '"2\n"'
argpos: 2
paramfile: boxshade.params
name: input_format
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Output parameters
name: output_params
children:
- !mobyle/inputprogramparameter
prompt: Output format
format: str(value) + "\n"
argpos: 3
paramfile: boxshade.params
mandatory: true
name: output_format
command: false
type: !mobyle/stringtype
default: e
options:
- {label: POSTSCRIPT (1), value: '1'}
- {label: Encapsulated POSTSCRIPT (2), value: '2'}
- {label: HPGL (3), value: '3'}
- {label: RTF (Rich Text Format) (4), value: '4'}
- {label: ANSI-screen (PC-version) (6), value: '6'}
- {label: VT100-screen (DEC-version) (7), value: '7'}
- {label: ReGIS-screen (25 lines each) (8), value: '8'}
- {label: ReGIS-file (without breaks) (9), value: '9'}
- {label: LJ250-printer file (a), value: a}
- {label: FIG file (for XFIG) (c), value: c}
- {label: PICT file (d), value: d}
- {label: HTML (e), value: e}
- !mobyle/inputprogramparameter
prompt: Should sequence name be printed
format: ( "n\n" , "y\n" )[ value ]
argpos: 13
paramfile: boxshade.params
name: print_name
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Display ruler line
format: ( "n\n" , "y\n" )[ value ]
argpos: 6
paramfile: boxshade.params
name: ruler
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Should position numbers be printed?
format: ( "n\n" , "y\n" )[ value ]
argpos: 14
paramfile: boxshade.params
name: print_position
precond: {'#not': ruler}
command: false
hidden: true
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: How many sequence characters per line
format: str( value ) + "\n"
argpos: 12
paramfile: boxshade.params
name: sequence_characters
command: false
type: !mobyle/integertype {default: 60}
- !mobyle/inputprogramparameter
prompt: How many lines between two sequence blocks
format: str(value) + "\n"
argpos: 17
paramfile: boxshade.params
name: lines
command: false
type: !mobyle/integertype {default: 1}
- !mobyle/inputprogramparameter
prompt: Character size in Points (except for HTML and ASCII output formats)
format: str(value) + "\n"
argpos: 28
paramfile: boxshade.params
name: character_size
precond:
output_format:
'#nin': ['8', '9', b, e]
command: false
type: !mobyle/integertype {default: 10}
- !mobyle/inputprogramparameter
prompt: Save Shading/Text
format: str(value) + "\n"
argpos: 29
paramfile: boxshade.params
mandatory: true
name: save_shading
precond: {output_format: d}
command: false
type: !mobyle/stringtype
default: T
options:
- {label: Save shading (S), value: S}
- {label: Save Shading+Text (T), value: T}
- !mobyle/inputprogramparameter
prompt: Rotate plot
format: ( "n\n" , "y\n" )[ value ]
argpos: 31
paramfile: boxshade.params
name: rotate
precond:
'#or':
- {output_format: '1'}
- {output_format: '3'}
- {output_format: d}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Sequence properties
name: sequence_params
children:
- !mobyle/inputprogramparameter
prompt: Special label for similar residues
format: ( "n\n" , "y\n" )[ value ]
argpos: 18
paramfile: boxshade.params
name: label_similar
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Special label for identical residues in all sequences
format: ( "n\n" , "y\n" )[ value ]
argpos: 19
paramfile: boxshade.params
name: label_identical
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Display consensus line
format: ( "n\n" , "y\n .*\n" )[ value ]
argpos: 5
paramfile: boxshade.params
name: consensus
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: The threshold is the fraction of residues that must be identical
or similar for shading to occur.
prompt: Identity threshold
format: str(value) + "\n"
argpos: 10
paramfile: boxshade.params
name: threshold
precond:
output_format: {'#ne': b}
command: false
type: !mobyle/floattype {default: 0.5}
- !mobyle/inputprogramparagraph
prompt: Letters foreground and background colors
name: letters
children:
- !mobyle/inputprogramparameter
prompt: Background for different residues
format: str(value) + "\n"
argpos: 20
paramfile: boxshade.params
mandatory: true
name: different_background
precond:
output_format: {'#ne': b}
command: false
type: !mobyle/stringtype
default: W
options:
- {label: Black (B), value: B}
- {label: White (W), value: W}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 (darkest)', value: '4'}
- {label: Red (R), value: R}
- {label: Green (G), value: G}
- {label: Blue (L), value: L}
- {label: Yellow (Y), value: Y}
- {label: Magenta (M), value: M}
- {label: Cyan (C), value: C}
- !mobyle/inputprogramparameter
prompt: Foreground for different residues (lowercase choices mean
lowercase letters in the sequence)
format: str(value) + "\n"
argpos: 21
paramfile: boxshade.params
mandatory: true
name: different_foreground
command: false
type: !mobyle/stringtype
default: B
options:
- {label: Black (B), value: B}
- {label: Black (b), value: b}
- {label: White (W), value: W}
- {label: White (w), value: w}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 = darkest', value: '4'}
- {label: 'Gray value: 5 (lowercase)', value: '5'}
- {label: 'Gray value: 6 (lowercase)', value: '6'}
- {label: 'Gray value: 7 (lowercase)', value: '7'}
- {label: 'Gray value: 8 = darkest (lowercase)', value: '8'}
- {label: Red (R), value: R}
- {label: Red (r), value: r}
- {label: Green (G), value: G}
- {label: Green (g), value: g}
- {label: Blue (L), value: L}
- {label: Blue (l), value: l}
- {label: Yellow (Y), value: Y}
- {label: Yellow (y), value: y}
- {label: Magenta (M), value: M}
- {label: Magenta (m), value: m}
- {label: Cyan (C), value: C}
- {label: Cyan (c), value: c}
- !mobyle/inputprogramparameter
prompt: Background for identical residues
format: str(value) + "\n"
argpos: 22
paramfile: boxshade.params
mandatory: true
name: identical_background
precond:
output_format: {'#ne': b}
command: false
type: !mobyle/stringtype
default: B
options:
- {label: Black (B), value: B}
- {label: White (W), value: W}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 (darkest)', value: '4'}
- {label: Red (R), value: R}
- {label: Green (G), value: G}
- {label: Blue (L), value: L}
- {label: Yellow (Y), value: Y}
- {label: Magenta (M), value: M}
- {label: Cyan (C), value: C}
- !mobyle/inputprogramparameter
prompt: Foreground for identical residues (lowercase choices mean
lowercase letters in the sequence)
format: str(value) + "\n"
argpos: 23
paramfile: boxshade.params
mandatory: true
name: identical_foreground
command: false
type: !mobyle/stringtype
default: W
options:
- {label: Black (B), value: B}
- {label: Black (b), value: b}
- {label: White (W), value: W}
- {label: White (w), value: w}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 = darkest', value: '4'}
- {label: 'Gray value: 5 (lowercase)', value: '5'}
- {label: 'Gray value: 6 (lowercase)', value: '6'}
- {label: 'Gray value: 7 (lowercase)', value: '7'}
- {label: 'Gray value: 8 = darkest (lowercase)', value: '8'}
- {label: Red (R), value: R}
- {label: Red (r), value: r}
- {label: Green (G), value: G}
- {label: Green (g), value: g}
- {label: Blue (L), value: L}
- {label: Blue (l), value: l}
- {label: Yellow (Y), value: Y}
- {label: Yellow (y), value: y}
- {label: Magenta (M), value: M}
- {label: Magenta (m), value: m}
- {label: Cyan (C), value: C}
- {label: Cyan (c), value: c}
- !mobyle/inputprogramparameter
prompt: Background for similar residues
format: str(value) + "\n"
argpos: 24
paramfile: boxshade.params
mandatory: true
name: similar_background
precond:
'#and':
- label_similar
- output_format: {'#ne': b}
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: Black (B), value: B}
- {label: White (W), value: W}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 (darkest)', value: '4'}
- {label: Red (R), value: R}
- {label: Green (G), value: G}
- {label: Blue (L), value: L}
- {label: Yellow (Y), value: Y}
- {label: Magenta (M), value: M}
- {label: Cyan (C), value: C}
- !mobyle/inputprogramparameter
prompt: Foreground for similar residues (lowercase choices mean lowercase
letters in the sequence)
format: str(value) + "\n"
argpos: 25
paramfile: boxshade.params
mandatory: true
name: similar_foreground
precond: label_similar
command: false
type: !mobyle/stringtype
default: B
options:
- {label: Black (B), value: B}
- {label: Black (b), value: b}
- {label: White (W), value: W}
- {label: White (w), value: w}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 = darkest', value: '4'}
- {label: 'Gray value: 5 (lowercase)', value: '5'}
- {label: 'Gray value: 6 (lowercase)', value: '6'}
- {label: 'Gray value: 7 (lowercase)', value: '7'}
- {label: 'Gray value: 8 = darkest (lowercase)', value: '8'}
- {label: Red (R), value: R}
- {label: Red (r), value: r}
- {label: Green (G), value: G}
- {label: Green (g), value: g}
- {label: Blue (L), value: L}
- {label: Blue (l), value: l}
- {label: Yellow (Y), value: Y}
- {label: Yellow (y), value: y}
- {label: Magenta (M), value: M}
- {label: Magenta (m), value: m}
- {label: Cyan (C), value: C}
- {label: Cyan (c), value: c}
- !mobyle/inputprogramparameter
prompt: Background for conserved residues (if special label for identical
residues)
format: str(value) + "\n"
argpos: 26
paramfile: boxshade.params
mandatory: true
name: conserved_background
precond:
'#and':
- label_identical
- output_format: {'#ne': b}
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: Black (B), value: B}
- {label: White (W), value: W}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 (darkest)', value: '4'}
- {label: Red (R), value: R}
- {label: Green (G), value: G}
- {label: Blue (L), value: L}
- {label: Yellow (Y), value: Y}
- {label: Magenta (M), value: M}
- {label: Cyan (C), value: C}
- !mobyle/inputprogramparameter
prompt: Foreground for conserved residues (lowercase choices mean
lowercase letters in the sequence)
format: str(value) + "\n"
argpos: 27
paramfile: boxshade.params
mandatory: true
name: conserved_foreground
precond: label_identical
command: false
type: !mobyle/stringtype
default: B
options:
- {label: Black (B), value: B}
- {label: Black (b), value: b}
- {label: White (W), value: W}
- {label: White (w), value: w}
- {label: 'Gray value: 1', value: '1'}
- {label: 'Gray value: 2', value: '2'}
- {label: 'Gray value: 3', value: '3'}
- {label: 'Gray value: 4 = darkest', value: '4'}
- {label: 'Gray value: 5 (lowercase)', value: '5'}
- {label: 'Gray value: 6 (lowercase)', value: '6'}
- {label: 'Gray value: 7 (lowercase)', value: '7'}
- {label: 'Gray value: 8 = darkest (lowercase)', value: '8'}
- {label: Red (R), value: R}
- {label: Red (r), value: r}
- {label: Green (G), value: G}
- {label: Green (g), value: g}
- {label: Blue (L), value: L}
- {label: Blue (l), value: l}
- {label: Yellow (Y), value: Y}
- {label: Yellow (y), value: y}
- {label: Magenta (M), value: M}
- {label: Magenta (m), value: m}
- {label: Cyan (C), value: C}
- {label: Cyan (c), value: c}
- !mobyle/inputprogramparagraph
prompt: Comparison to a single sequence
name: single_comparison
children:
- !mobyle/inputprogramparameter
prompt: Similarity to a single sequence
format: ( "n\n" , "y\n" )[ value ]
argpos: 4
paramfile: boxshade.params
name: single
precond:
output_format: {'#ne': b}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Which sequence (give its number)
format: str(value) + "\n"
argpos: 40
paramfile: boxshade.params
mandatory: true
name: seq_no
precond: single
command: false
type: !mobyle/integertype {default: 1}
- !mobyle/inputprogramparameter
prompt: Hide this sequence
format: ( "n\n" , "y\n" )[ value ]
argpos: 41
paramfile: boxshade.params
name: hide
precond: single
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Show this sequence in all-normal rendition
format: ( "n\n" , "y\n" )[ value ]
argpos: 42
paramfile: boxshade.params
name: show_normal
precond: single
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Create identity / similarity matrix
format: ( "n\n" , "y\n" )[ value ]
argpos: 34
paramfile: boxshade.params
name: matrix
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
format: '"boxshade.result\n"'
argpos: 32
paramfile: boxshade.params
name: outfileName
precond:
'#and':
- output_format: {'#ne': '1'}
- output_format: {'#ne': e}
- output_format: {'#ne': '2'}
- output_format: {'#ne': d}
- output_format: {'#ne': c}
- output_format: {'#ne': '4'}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.ps\n"'
argpos: 33
paramfile: boxshade.params
name: psFileName
precond:
'#or':
- {output_format: '1'}
- {output_format: '2'}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.html\n"'
argpos: 33
paramfile: boxshade.params
name: htmlFileName
precond: {output_format: e}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.rtf\n"'
argpos: 33
paramfile: boxshade.params
name: rtfFileName
precond: {output_format: '4'}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.fig\n"'
argpos: 33
paramfile: boxshade.params
name: figFileName
precond: {output_format: c}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.pict\n"'
argpos: 33
paramfile: boxshade.params
name: pictFileName
precond: {output_format: d}
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"boxshade.matrix\n"'
argpos: 35
paramfile: boxshade.params
name: matrixFileName
precond: matrix
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Output file
filenames: '"boxshade.result"'
name: outFile
precond:
'#and':
- output_format: {'#ne': '1'}
- output_format: {'#ne': e}
- output_format: {'#ne': '2'}
- output_format: {'#ne': d}
- output_format: {'#ne': c}
- output_format: {'#ne': '4'}
- !mobyle/outputprogramparameter
prompt: Postscript output file
filenames: '"boxshade.ps"'
name: psFile
precond:
'#or':
- {output_format: '1'}
- {output_format: '2'}
- !mobyle/outputprogramparameter
prompt: Html output file
filenames: '"boxshade.html"'
name: htmlFile
precond: {output_format: e}
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Rich text format output file
filenames: '"boxshade.rtf"'
name: rtfFile
precond: {output_format: '4'}
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Xfig output file
filenames: '"boxshade.fig"'
name: figFile
precond: {output_format: c}
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Picture in pict format
filenames: '"boxshade.pict"'
name: pictFile
precond: {output_format: d}
- !mobyle/outputprogramparameter {prompt: Output matrix, filenames: '"boxshade.matrix"',
name: matrixFile, precond: matrix}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"boxshade.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"boxshade.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0565']
topics: ['EDAM_topic:0092']
homepage_links: ['http://www.ch.embnet.org/software/BOX_form.html']
env: {}
source_links: ['ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/']