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distmat.yaml
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distmat.yaml
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!mobyle/program
name: distmat
title: distmat
description: Create a distance matrix from a multiple sequence alignment
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
comment: File containing a sequence alignment.
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:2200', 'EDAM_format:1993', 'EDAM_format:1996',
'EDAM_format:1985', 'EDAM_format:1986', 'EDAM_format:1988', 'EDAM_format:1989',
'EDAM_format:1987', 'EDAM_format:2002', 'EDAM_format:2003', 'EDAM_format:1999',
'EDAM_format:2001', 'EDAM_format:2001', 'EDAM_format:2001', 'EDAM_format:1990']
data_terms: ['EDAM_data:0863']
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
comment: Multiple substitution correction methods for nucleotides.
prompt: Multiple substitution correction methods for nucleotides
format: ("", " -nucmethod=" + str(value))[value is not None and value!=vdef]
argpos: 2
name: nucmethod
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: Uncorrected, value: '0'}
- {label: Jukes-cantor, value: '1'}
- {label: Kimura, value: '2'}
- {label: Tamura, value: '3'}
- {label: Tajima-nei, value: '4'}
- {label: Jin-nei gamma, value: '5'}
- !mobyle/inputprogramparameter
comment: Multiple substitution correction methods for proteins.
prompt: Multiple substitution correction methods for proteins
format: ("", " -protmethod=" + str(value))[value is not None and value!=vdef]
argpos: 3
name: protmethod
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: Uncorrected, value: '0'}
- {label: Jukes-cantor, value: '1'}
- {label: Kimura protein, value: '2'}
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
comment: Option to use the ambiguous codes in the calculation of the Jukes-Cantor
method or if the sequences are proteins.
prompt: Use the ambiguous codes in the calculation.
format: ("", " -ambiguous")[ bool(value) ]
argpos: 4
name: ambiguous
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor
distance methods.
prompt: Weight given to gaps
format: ("", " -gapweight=" + str(value))[value is not None and value!=vdef]
argpos: 5
name: gapweight
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
comment: Choose base positions to analyse in each codon i.e. 123 (all
bases), 12 (the first two bases), 1, 2, or 3 individual bases.
prompt: Base position to analyse
format: ("", " -position=" + str(value))[value is not None and value!=vdef]
argpos: 6
name: position
command: false
type: !mobyle/integertype {default: 123}
- !mobyle/inputprogramparameter
comment: This will force the calculation of parameter 'a' in the Jin-Nei
Gamma distance calculation, otherwise the default is 1.0 (see -parametera
option).
prompt: Calculate the nucleotide jin-nei parameter 'a'
format: ("", " -calculatea")[ bool(value) ]
argpos: 7
name: calculatea
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: User defined parameter 'a' to be use in the Jin-Nei Gamma distance
calculation. The suggested value to be used is 1.0 (Jin et al.) and
this is the default.
prompt: Nucleotide jin-nei parameter 'a'
format: ("", " -parametera=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: parametera
command: false
type: !mobyle/floattype {default: 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: 9
name: outfile
command: false
type: !mobyle/stringtype {default: distmat.outfile}
- !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: Outfile_out option, filenames: outfile,
name: outfile_out}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"distmat.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"distmat.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0289']
topics: ['EDAM_topic:0159', 'EDAM_topic:0084']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/distmat.html', 'http://emboss.sourceforge.net/docs/themes']
command: distmat
env: {}