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compseq.yaml
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compseq.yaml
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!mobyle/program
name: compseq
title: compseq
description: Calculate the composition of unique words in sequences
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:2044']
- !mobyle/inputprogramparameter
comment: "This is a file previously produced by 'compseq' that can be\
\ used to set the expected frequencies of words in this analysis.\
\ \n The word size in the current run must be the same as the one\
\ in this results file. Obviously, you should use a file produced\
\ from protein sequences if you are counting protein sequence word\
\ frequencies, and you must use one made from nucleotide frequencies\
\ if you are analysing a nucleotide sequence."
prompt: Program compseq output file (optional)
format: ("", " -infile=" + str(value))[value is not None]
argpos: 2
name: infile
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
comment: "This is the size of word (n-mer) to count. \n Thus if you want\
\ to count codon frequencies for a nucleotide sequence, you should\
\ enter 3 here."
prompt: Word size to consider (e.g. 2=dimer) (value greater than or equal
to 1)
format: ("", " -word=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: word
command: false
type: !mobyle/integertype {default: 2}
ctrls:
- message: Value greater than or equal to 1 is required
test:
value: {'#gte': '1'}
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
comment: "The normal behaviour of 'compseq' is to count the frequencies\
\ of all words that occur by moving a window of length 'word' up\
\ by one each time. \n This option allows you to move the window\
\ up by the length of the word each time, skipping over the intervening\
\ words. \n You can count only those words that occur in a single\
\ frame of the word by setting this value to a number other than\
\ zero. \n If you set it to 1 it will only count the words in frame\
\ 1, 2 will only count the words in frame 2 and so on."
prompt: Frame of word to look at (0=all frames) (value greater than or
equal to 0)
format: ("", " -frame=" + str(value))[value is not None and value!=vdef]
argpos: 4
name: frame
command: false
type: !mobyle/integertype {default: 0}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparameter
comment: "The amino acid code B represents Asparagine or Aspartic acid\
\ and the code Z represents Glutamine or Glutamic acid. \n These\
\ are not commonly used codes and you may wish not to count words\
\ containing them, just noting them in the count of 'Other' words."
prompt: Ignore the amino acids b and z and just count them as 'other'
format: (" -noignorebz", "")[ bool(value) ]
argpos: 5
name: ignorebz
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Set this to be true if you also wish to also count words in the
reverse complement of a nucleic sequence.
prompt: Count words in the forward and reverse sense
format: ("", " -reverse")[ bool(value) ]
argpos: 6
name: reverse
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "If this is set true then the expected frequencies of words are\
\ calculated from the observed frequency of single bases or residues\
\ in the sequences. \n If you are reporting a word size of 1 (single\
\ bases or residues) then there is no point in using this option\
\ because the calculated expected frequency will be equal to the\
\ observed frequency. \n Calculating the expected frequencies like\
\ this will give an approximation of the expected frequencies that\
\ you might get by using an input file of frequencies produced by\
\ a previous run of this program. If an input file of expected word\
\ frequencies has been specified then the values from that file will\
\ be used instead of this calculation of expected frequency from\
\ the sequence, even if 'calcfreq' is set to be true."
prompt: Calculate expected frequency from sequence
format: ("", " -calcfreq")[ bool(value) ]
argpos: 7
name: calcfreq
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: This is the results file.
prompt: Name of the output file (outfile)
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 8
name: outfile
command: false
type: !mobyle/stringtype {default: outfile.composition}
- !mobyle/inputprogramparameter
comment: You can make the output results file much smaller if you do not
display the words with a zero count.
prompt: Display the words that have a frequency of zero
format: (" -nozerocount", "")[ bool(value) ]
argpos: 9
name: zerocount
command: false
type: !mobyle/booleantype {default: false}
- !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
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"compseq.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"compseq.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0236']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/compseq.html', 'http://emboss.sourceforge.net/docs/themes']
command: compseq
env: {}