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emowse.yaml
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!mobyle/program
name: emowse
title: emowse
description: Search protein sequences by digest fragment molecular weight
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Sequence option
format: ("", " -sequence=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: sequence
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:2976']
- !mobyle/inputprogramparameter {prompt: Peptide molecular weight values file,
format: '("", " -infile=" + str(value))[value is not None]', simple: true,
argpos: 2, mandatory: true, name: infile, command: false}
- !mobyle/inputprogramparameter {prompt: Molecular weights data file, format: '("",
" -mwdata=" + str(value))[value is not None ]', argpos: 3, name: mwdata,
command: false}
- !mobyle/inputprogramparameter {prompt: Amino acid frequencies data file,
format: '("", " -frequencies=" + str(value))[value is not None ]', argpos: 4,
name: frequencies, command: false}
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
prompt: Whole sequence molwt
format: ("", " -weight=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 5
mandatory: true
name: weight
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparameter
prompt: Use monoisotopic weights
format: ("", " -mono")[ bool(value) ]
argpos: 6
name: mono
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Advanced section
name: advanced
children:
- !mobyle/inputprogramparameter
prompt: Enzymes and reagents
format: ("", " -enzyme=" + str(value))[value is not None and value!=vdef]
argpos: 7
name: enzyme
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: Trypsin, value: '1'}
- {label: Lys-c, value: '2'}
- {label: Arg-c, value: '3'}
- {label: Asp-n, value: '4'}
- {label: V8-bicarb, value: '5'}
- {label: V8-phosph, value: '6'}
- {label: Chymotrypsin, value: '7'}
- {label: Cnbr, value: '8'}
- !mobyle/inputprogramparameter
prompt: Allowed whole sequence weight variability (value from 0 to 75)
format: ("", " -pcrange=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: pcrange
command: false
type: !mobyle/integertype {default: 25}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- message: Value less than or equal to 75 is required
test:
value: {'#lte': '75'}
- !mobyle/inputprogramparameter
prompt: Tolerance (value from 0.1 to 1.0)
format: ("", " -tolerance=" + str(value))[value is not None and value!=vdef]
argpos: 9
name: tolerance
command: false
type: !mobyle/floattype {default: 0.1}
ctrls:
- message: Value greater than or equal to 0.1 is required
test:
value: {'#gte': '0.1'}
- message: Value less than or equal to 1.0 is required
test:
value: {'#lte': '1.0'}
- !mobyle/inputprogramparameter
prompt: Partials factor (value from 0.1 to 1.0)
format: ("", " -partials=" + str(value))[value is not None and value!=vdef]
argpos: 10
name: partials
command: false
type: !mobyle/floattype {default: 0.4}
ctrls:
- message: Value greater than or equal to 0.1 is required
test:
value: {'#gte': '0.1'}
- message: Value less than or equal to 1.0 is required
test:
value: {'#lte': '1.0'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
prompt: Name of the output file (outfile)
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 11
name: outfile
command: false
type: !mobyle/stringtype {default: emowse.outfile}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 12
name: auto
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/outputprogramparameter
prompt: Outfile_out option
filenames: outfile
name: outfile_out
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"emowse.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"emowse.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0356']
topics: ['EDAM_topic:0123', 'EDAM_topic:0141']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/emowse.html', 'http://emboss.sourceforge.net/docs/themes']
command: emowse
env: {}