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edialign.yaml
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edialign.yaml
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!mobyle/program
name: edialign
title: edialign
description: Local multiple alignment of sequences
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Sequences option
format: ("", " -sequences=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: sequences
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: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
comment: Nucleic acid sequence alignment mode (simple, translated or mixed)
prompt: Nucleic acid sequence alignment mode
format: ("", " -nucmode=" + str(value))[value is not None and value!=vdef]
argpos: 2
name: nucmode
command: false
type: !mobyle/stringtype
default: n
options:
- {label: Simple, value: n}
- {label: Translation, value: nt}
- {label: Mixed alignments, value: ma}
- !mobyle/inputprogramparameter
prompt: Also consider the reverse complement
format: ("", " -revcomp")[ bool(value) ]
argpos: 3
name: revcomp
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: By default overlap weights are used when Nseq =<35 but you can
set this to 'yes' or 'no'
prompt: Use overlap weights
format: ("", " -overlapw=" + str(value))[value is not None and value!=vdef]
argpos: 4
name: overlapw
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: Default (when nseq =< 35), value: '1'}
- {label: 'Yes', value: '2'}
- {label: 'No', value: '3'}
- !mobyle/inputprogramparameter
comment: Clustering method to construct sequence tree (UPGMA, minimum
linkage or maximum linkage)
prompt: Clustering method to construct sequence tree
format: ("", " -linkage=" + str(value))[value is not None and value!=vdef]
argpos: 5
name: linkage
command: false
type: !mobyle/stringtype
default: UPGMA
options:
- {label: Upgma, value: UPGMA}
- {label: Maximum linkage, value: max}
- {label: Minimum linkage, value: min}
- !mobyle/inputprogramparameter
prompt: Maximum fragment length (value greater than or equal to 0)
format: ("", " -maxfragl=" + str(value))[value is not None and value!=vdef]
argpos: 6
name: maxfragl
command: false
type: !mobyle/integertype {default: 40}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparameter
prompt: Consider only n-fragment pairs that start with two matches
format: ("", " -fragmat")[ bool(value) ]
argpos: 7
name: fragmat
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Consider only p-fragment pairs if first amino acid or codon pair
has similarity score of at least n (value greater than or equal to
0)
format: ("", " -fragsim=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: fragsim
command: false
type: !mobyle/integertype {default: 4}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparameter
prompt: Use iterative score
format: ("", " -itscore")[ bool(value) ]
argpos: 9
name: itscore
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Threshold for considering diagonal for alignment (value greater
than or equal to 0.0)
format: ("", " -threshold=" + str(value))[value is not None and value!=vdef]
argpos: 10
name: threshold
command: false
type: !mobyle/floattype {default: 0.0}
ctrls:
- message: Value greater than or equal to 0.0 is required
test:
value: {'#gte': '0.0'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
prompt: Replace unaligned characters by stars '*' rather then putting
them in lowercase
format: ("", " -mask")[ bool(value) ]
argpos: 11
name: mask
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Activate writing of stars instead of numbers
format: ("", " -dostars")[ bool(value) ]
argpos: 12
name: dostars
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Put up to n stars '*' instead of digits 0-9 to indicate level
of conservation (value greater than or equal to 0)
format: ("", " -starnum=" + str(value))[value is not None and value!=vdef]
argpos: 13
name: starnum
command: false
type: !mobyle/integertype {default: 4}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparameter
prompt: Name of the output file (outfile)
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 14
name: outfile
command: false
type: !mobyle/stringtype {default: edialign.outfile}
- !mobyle/inputprogramparameter
prompt: Name of the output sequence file (outseq)
format: ("" , " -outseq=" + str(value))[value is not None]
argpos: 15
name: outseq
command: false
type: !mobyle/stringtype {default: edialign.outseq}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 16
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: Outseq_out option, filenames: outseq,
name: outseq_out}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"edialign.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"edialign.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0495']
topics: ['EDAM_topic:0186']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/edialign.html', 'http://emboss.sourceforge.net/docs/themes']
command: edialign
env: {}