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dottup.yaml
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dottup.yaml
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!mobyle/program
name: dottup
title: dottup
description: Displays a wordmatch dotplot of two sequences
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Asequence option
format: ("", " -asequence=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: asequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1927', 'EDAM_format:2200', 'EDAM_format:1935',
'EDAM_format:1936', 'EDAM_format:1948', 'EDAM_format:1948', 'EDAM_format:1957',
'EDAM_format:2188']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Bsequence option
format: ("", " -bsequence=" + str(value))[value is not None]
simple: true
argpos: 2
mandatory: true
name: bsequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1927', 'EDAM_format:2200', 'EDAM_format:1935',
'EDAM_format:1936', 'EDAM_format:1948', 'EDAM_format:1948', 'EDAM_format:1957',
'EDAM_format:2188']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
prompt: Word size (value greater than or equal to 2)
format: ("", " -wordsize=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: wordsize
command: false
type: !mobyle/integertype {default: 10}
ctrls:
- message: Value greater than or equal to 2 is required
test:
value: {'#gte': '2'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: Use non-proportional axes
prompt: Stretch axes
format: ("", " -stretch")[ bool(value) ]
argpos: 4
name: stretch
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Choose the graph output format
format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
None and value!=vdef]
argpos: 5
name: graph
precond: {'#not': stretch}
command: false
type: !mobyle/stringtype
default: png
options:
- {label: Png, value: png}
- {label: Gif, value: gif}
- {label: Cps, value: cps}
- {label: Ps, value: ps}
- {label: Meta, value: meta}
- {label: Data, value: data}
- !mobyle/inputprogramparameter
prompt: Name of the output graph
format: ("" , " -goutfile=" + str(value))[value is not None]
argpos: 6
name: goutfile
precond: {'#not': stretch}
command: false
type: !mobyle/stringtype {default: dottup_graph}
- !mobyle/inputprogramparameter
prompt: Choose the xygraph output format
format: (" -xygraph=" + str(vdef), " -xygraph=" + str(value))[value is
not None and value!=vdef]
argpos: 7
name: xygraph
precond: stretch
command: false
type: !mobyle/stringtype
default: png
options:
- {label: Png, value: png}
- {label: Gif, value: gif}
- {label: Cps, value: cps}
- {label: Ps, value: ps}
- {label: Meta, value: meta}
- {label: Data, value: data}
- !mobyle/inputprogramparameter
prompt: Name of the output graph
format: ("" , " -goutfile=" + str(value))[value is not None]
argpos: 8
name: xy_goutfile
precond: stretch
command: false
type: !mobyle/stringtype {default: dottup_xygraph}
- !mobyle/inputprogramparameter
prompt: Draw a box around dotplot
format: (" -noboxit", "")[ bool(value) ]
argpos: 9
name: boxit
precond: {'#not': stretch}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 10
name: auto
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.png"'
name: outgraph_png
precond:
'#and':
- {'#not': stretch}
- {graph: png}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.gif"'
name: outgraph_gif
precond:
'#and':
- {'#not': stretch}
- {graph: gif}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.ps"'
name: outgraph_ps
precond:
'#or':
- '#and':
- {'#not': stretch}
- {graph: ps}
- {graph: cps}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.meta"'
name: outgraph_meta
precond:
'#and':
- {'#not': stretch}
- {graph: meta}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.dat"'
name: outgraph_data
precond:
'#and':
- {'#not': stretch}
- {graph: data}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.png"'
name: xy_outgraph_png
precond:
'#and':
- stretch
- {xygraph: png}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.gif"'
name: xy_outgraph_gif
precond:
'#and':
- stretch
- {xygraph: gif}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.ps"'
name: xy_outgraph_ps
precond:
'#or':
- '#and':
- stretch
- {xygraph: ps}
- {xygraph: cps}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.meta"'
name: xy_outgraph_meta
precond:
'#and':
- stretch
- {xygraph: meta}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.dat"'
name: xy_outgraph_data
precond:
'#and':
- stretch
- {xygraph: data}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"dottup.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"dottup.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0288', 'EDAM_operation:0490']
topics: ['EDAM_topic:0159']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/dottup.html', 'http://emboss.sourceforge.net/docs/themes']
command: dottup
env: {}