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dca_1.1.yaml
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dca_1.1.yaml
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!mobyle/program
name: dca
version: '1.1'
title: DCA
description: Divide-and-Conquer Multiple Sequence Alignment
authors: J. Stoye
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
prompt: Sequences File
format: '" "+str(value)'
simple: true
argpos: 100
mandatory: true
name: seq
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparagraph
prompt: Control parameters
name: control
children:
- !mobyle/inputprogramparameter
prompt: Cost matrix (-c)
format: ( "" , " -c " + str(value) )[ value is not None and value !=
vdef]
argpos: 1
name: cost
command: false
type: !mobyle/stringtype
default: 'null'
options:
- {label: 'Default: depends on sequences', value: 'null'}
- {label: BLOSUM30, value: blosum30}
- {label: BLOSUM45, value: blosum45}
- {label: BLOSUM62, value: blosum62}
- {label: PAM160, value: pam160}
- {label: PAM250, value: pam250}
- {label: Unitcost, value: unitcost}
- {label: DNA, value: dna}
- {label: RNA, value: rna}
- {label: DNA/RNA, value: dnarna}
- !mobyle/inputprogramparameter
comment: 'Default: free shift'
prompt: Penalize end gaps as internal gaps (-g)
format: ("" , " -g ")[ value ]
argpos: 1
name: gaps
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: 'On: FastDCA (use approximate cut positions); Off: slower, more
accurate algorithm (search for exact cut positions)'
prompt: Use approximate cut positions (-a)
format: ("" , " -a")[ value ]
argpos: 1
name: approximate
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Weight intensity (-b)
format: ( "" , " -b " + str(value) )[ value is not None and value !=
vdef]
argpos: 1
name: intensity
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
comment: '5 ... 100 recommended; small: faster algorithm, maybe worse.'
prompt: Recursion stop size (-l)
format: ( "" , " -l " + str(value) )[ value is not None and value !=
vdef]
argpos: 1
name: recursion
command: false
type: !mobyle/integertype {default: 30}
- !mobyle/inputprogramparameter
comment: To correct the alignment in the proximity of division sites,
the sequences can be re-aligned inside a window of size w >= 0 placed
across each slicing site.
prompt: Window size (-w)
format: ( "" , " -w " + str(value) )[ value is not None and value !=
vdef]
argpos: 1
name: window
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparagraph
prompt: Output parameters
name: output
children:
- !mobyle/inputprogramparameter
format: '" -q"'
argpos: 1
name: quiet
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Output format (-f)
format: ( "" , " -f " + str(value) )[ value is not None and value !=
vdef]
argpos: 1
name: output_format
command: false
type: !mobyle/stringtype
default: '2'
options:
- {label: aln (1), value: '1'}
- {label: fasta (2), value: '2'}
- {label: nex (3), value: '3'}
- {label: dca (4), value: '4'}
- !mobyle/inputprogramparameter
prompt: Suppress output about progress of the program (-o)
format: '" -o"'
argpos: 1
name: suppress_output
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Alignment file
filenames: '"dca.out"'
name: fasta_outfile
precond:
'#or':
- {output_format: '2'}
- {output_format: '3'}
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:0863']
- !mobyle/outputprogramparameter
prompt: DCA alignment file
filenames: '"dca.out"'
name: aln_outfile
precond:
'#or':
- {output_format: '1'}
- {output_format: '4'}
output_type: stdout
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"dca.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
comment: Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing
fast, high quality simultaneous multiple sequence alignments of amino acid, RNA,
or DNA sequences. The program is based on the DCA algorithm, a heuristic approach
to sum-of-pairs (SP) optimal alignment that has been developed at the FSPM over
the years 1995-97.
operations: ['EDAM_operation:0492']
topics: ['EDAM_topic:0182']
references:
- {doi: null, label: 'A.W.M. Dress, G. Fullen, S.W. Perrey, A Divide and Conquer Approach
to Multiple Alignment, Proceedings of the Third International Conference on
Intelligent Systems for Molecular Biology (ISMB 95), AAAI Press, Menlo Park,
CA, USA, 107-113, 1995.', url: null}
- {doi: null, label: 'J. Stoye, Multiple Sequence Alignment with the Divide-and-Conquer
Method, Gene 211(2), GC45-GC56, 1998. (Gene-COMBIS)', url: null}
homepage_links: ['http://bibiserv.techfak.uni-bielefeld.de/dca/']
command: dca
env: {}
source_links: ['http://bibiserv.techfak.uni-bielefeld.de/download/tools/dca.html']