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dotmatcher.yaml
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!mobyle/program
name: dotmatcher
title: dotmatcher
description: Draw a threshold 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/inputprogramparameter
comment: This is the scoring matrix file used when comparing sequences.
By default it is the file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These files are found in the
'data' directory of the EMBOSS installation.
prompt: Matrix file
format: ("", " -matrixfile=" + str(value))[value is not None and value!=vdef]
argpos: 3
name: matrixfile
command: false
type: !mobyle/stringtype
default: mobyle_null
options:
- {label: null, value: mobyle_null}
- {label: Eblosum30, value: EBLOSUM30}
- {label: Eblosum35, value: EBLOSUM35}
- {label: Eblosum40, value: EBLOSUM40}
- {label: Eblosum45, value: EBLOSUM45}
- {label: Eblosum50, value: EBLOSUM50}
- {label: Eblosum55, value: EBLOSUM55}
- {label: Eblosum60, value: EBLOSUM60}
- {label: Eblosum62, value: EBLOSUM62}
- {label: Eblosum62-12, value: EBLOSUM62-12}
- {label: Eblosum65, value: EBLOSUM65}
- {label: Eblosum70, value: EBLOSUM70}
- {label: Eblosum75, value: EBLOSUM75}
- {label: Eblosum80, value: EBLOSUM80}
- {label: Eblosum85, value: EBLOSUM85}
- {label: Eblosum90, value: EBLOSUM90}
- {label: Eblosumn, value: EBLOSUMN}
- {label: Ednafull, value: EDNAFULL}
- {label: Ednamat, value: EDNAMAT}
- {label: Ednasimple, value: EDNASIMPLE}
- {label: Epam10, value: EPAM10}
- {label: Epam100, value: EPAM100}
- {label: Epam110, value: EPAM110}
- {label: Epam120, value: EPAM120}
- {label: Epam130, value: EPAM130}
- {label: Epam140, value: EPAM140}
- {label: Epam150, value: EPAM150}
- {label: Epam160, value: EPAM160}
- {label: Epam170, value: EPAM170}
- {label: Epam180, value: EPAM180}
- {label: Epam190, value: EPAM190}
- {label: Epam20, value: EPAM20}
- {label: Epam200, value: EPAM200}
- {label: Epam210, value: EPAM210}
- {label: Epam220, value: EPAM220}
- {label: Epam230, value: EPAM230}
- {label: Epam240, value: EPAM240}
- {label: Epam250, value: EPAM250}
- {label: Epam260, value: EPAM260}
- {label: Epam270, value: EPAM270}
- {label: Epam280, value: EPAM280}
- {label: Epam290, value: EPAM290}
- {label: Epam30, value: EPAM30}
- {label: Epam300, value: EPAM300}
- {label: Epam310, value: EPAM310}
- {label: Epam320, value: EPAM320}
- {label: Epam330, value: EPAM330}
- {label: Epam340, value: EPAM340}
- {label: Epam350, value: EPAM350}
- {label: Epam360, value: EPAM360}
- {label: Epam370, value: EPAM370}
- {label: Epam380, value: EPAM380}
- {label: Epam390, value: EPAM390}
- {label: Epam40, value: EPAM40}
- {label: Epam400, value: EPAM400}
- {label: Epam410, value: EPAM410}
- {label: Epam420, value: EPAM420}
- {label: Epam430, value: EPAM430}
- {label: Epam440, value: EPAM440}
- {label: Epam450, value: EPAM450}
- {label: Epam460, value: EPAM460}
- {label: Epam470, value: EPAM470}
- {label: Epam480, value: EPAM480}
- {label: Epam490, value: EPAM490}
- {label: Epam50, value: EPAM50}
- {label: Epam500, value: EPAM500}
- {label: Epam60, value: EPAM60}
- {label: Epam70, value: EPAM70}
- {label: Epam80, value: EPAM80}
- {label: Epam90, value: EPAM90}
- {label: Sssub, value: SSSUB}
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
prompt: Window size over which to test threshold (value greater than or
equal to 3)
format: ("", " -windowsize=" + str(value))[value is not None and value!=vdef]
argpos: 4
name: windowsize
command: false
type: !mobyle/integertype {default: 10}
ctrls:
- message: Value greater than or equal to 3 is required
test:
value: {'#gte': '3'}
- !mobyle/inputprogramparameter
prompt: Threshold (value greater than or equal to 0)
format: ("", " -threshold=" + str(value))[value is not None and value!=vdef]
argpos: 5
name: threshold
command: false
type: !mobyle/integertype {default: 23}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: Display a non-proportional graph
prompt: Stretch plot
format: ("", " -stretch")[ bool(value) ]
argpos: 6
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: 7
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: 8
name: goutfile
precond: {'#not': stretch}
command: false
type: !mobyle/stringtype {default: dotmatcher_graph}
- !mobyle/inputprogramparameter
prompt: Choose the xygraph output format
format: (" -xygraph=" + str(vdef), " -xygraph=" + str(value))[value is
not None and value!=vdef]
argpos: 9
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: 10
name: xy_goutfile
precond: stretch
command: false
type: !mobyle/stringtype {default: dotmatcher_xygraph}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 11
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: '"dotmatcher.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"dotmatcher.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0490']
topics: ['EDAM_topic:0159']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/dotmatcher.html', 'http://emboss.sourceforge.net/docs/themes']
command: dotmatcher
env: {}