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dialign_2.2.1.yaml
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dialign_2.2.1.yaml
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!mobyle/program
name: dialign
version: 2.2.1
title: DIALIGN
description: DNA and protein sequence alignment based on segment-to-segment comparison
authors: Morgenstern, Dress, Werner
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
prompt: Sequences
format: '" " + str(value)'
simple: true
argpos: 100
mandatory: true
name: sequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Nucleic acid or protein alignment (-n)
format: ( "" , " -n" )[ value is not None and value != vdef]
simple: true
argpos: 2
mandatory: true
name: protein_dna
command: false
type: !mobyle/stringtype
default: p
options:
- {label: Protein (p), value: p}
- {label: Nucleic (n), value: n}
- !mobyle/inputprogramparagraph
prompt: Others options
name: dialign_opt
argpos: 3
children:
- !mobyle/inputprogramparameter
prompt: Threshold (-thr)
format: ( "" , " -thr " + str(value) )[ value is not None and value !=
vdef]
name: threshold
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
comment: '"maximum or minimum linkage" clustering used to construct sequence
tree (instead of UPGMA).'
prompt: Clustering type used to construct sequence tree
format: ( "" , " -" +str(value) )[ value is not None and value !=vdef]
name: cluster
command: false
type: !mobyle/stringtype
default: 'null'
options:
- {label: UPGMA, value: 'null'}
- {label: Maximum linkage (-max_link), value: max_link}
- {label: Minimum linkage (-min_link), value: min_link}
- !mobyle/inputprogramparameter
comment: "iterative scoring scheme (fragment scores are based on\n \
\ conditional probabilities given the previously aligned\n\
\ fragments. I.e. the probability of a fragment --\
\ and\n therefore its score -- is not based on the\
\ probability\n of random occurrence in the input\
\ sequences but rather on\n the probability of occurrence\
\ between those fragments\n that have already been\
\ accepted in previous iteration\n steps)."
prompt: Iterative scoring scheme (-it)
format: ( "" , " -it" )[ value ]
name: iterative
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "overlap weights switched off (by default,\n \
\ overlap weights are used if up to 35 sequences are\n \
\ aligned). This option speeds up the alignment but may lead\n\
\ to reduced alignment quality."
prompt: Overlap weights (-iw)
format: ( "" , " -iw" )[ value ]
name: overlap
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: DNA options
name: dna_opt
precond: {protein_dna: n}
children:
- !mobyle/inputprogramparameter
comment: Input sequences are nucleic acid sequences and `nucleic acid
segments' are translated to `peptide segments'.
prompt: Translation of nucleotide diagonals into peptide diagonals
(-nt)
format: ( "" , " -nt" )[ value ]
name: translation
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: If segments are translated, not only the `Watson strand'
but also the `Crick strand' is looked at
prompt: Strand to looked at Watson and Crick strands (-cs)
format: ( "" , " -cs" )[ value ]
name: translation_strand
precond:
'#or': [translation, mix]
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: '`mixed alignments'' consisting of P-fragments and N-fragments
if nucleic acid sequences are aligned.'
prompt: Mixed alignments (-ma)
format: ( "" , " -ma" )[ value ]
name: mix
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "Non-translated nucleic acid fragments are taken\n \
\ into account only if they start with at least two\
\ matches.\n Speeds up DNA alignment at the expense\
\ of sensitivity."
prompt: Dna alignment speed up (-ds)
format: ( "" , " -ds" )[ value ]
name: speed
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "combines the following options:\n -ma, -it,\
\ -thr 2, -lmax 30, -smin 8, -nta, -ff,\n -fop,\
\ -ff, -cs, -ds, -pst"
prompt: Long genomic sequences (-lgs)
format: ( "" , " -lgs" )[ value ]
name: long_genomic
precond: {'#not': long_genomic_pep}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Like "-lgs" but with all segment pairs assessed at the peptide
level (rather than 'mixed alignments' as with the"-lgs" option).
Therefore faster than -lgs but not very sensitive for non-coding
regions.
prompt: Long genomic sequences (-lfs_t)
format: ( "" , " -lgs_t" )[ value ]
name: long_genomic_pep
precond: {'#not': long_genomic}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Output options
name: output_options
argpos: 3
children:
- !mobyle/inputprogramparameter
comment: 'The number of `*'' characters below the alignment reflects the
degree of local similarity among sequences. More precisely: They represent
the sum of `weights'' of diagonals connecting residues at the respective
position.By default, no stars are used but numbers between 0 and 9,
instead.'
prompt: Maximum number of * characters representing degree similarity
(-stars)
format: ( "" , " -stars " + str(value) )[ value is not None]
name: max_simil
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
comment: residues not belonging to selected fragments are replaced by
`*' characters in output alignment (rather than being printed in lower-case
characters)
prompt: Mask not aligned residues (-mask)
format: ( "" , " -mask" )[ value ]
name: mask
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Be aware that only upper-case letters are regarded to be aligned
in fasta output file.
prompt: Alignment in fasta format (-fa)
format: ( "" , " -fa" )[ value ]
name: fasta
command: false
type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter {prompt: Output file, filenames: '"*.cw"', name: ali}
- !mobyle/outputprogramparameter
prompt: fasta alignment file
filenames: '"*.fa"'
name: fasta_alignment
precond: fasta
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:0863']
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"dialign.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"dialign.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0492']
topics: ['EDAM_topic:0182']
references:
- {doi: null, label: 'B. Morgenstern (1999). DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment. Bioinformatics 15, 211 - 218.', url: null}
homepage_links: ['http://dialign.gobics.de/']
command: dialign
env: {}
source_links: ['http://dialign.gobics.de/download/']