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cif_0.2.2.yaml
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cif_0.2.2.yaml
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!mobyle/program
name: cif
version: 0.2.2
title: CIF
description: Cut DNA regions in frame
authors: E. Quevillon, B. Boeda
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Sequence
format: ( "" , " -i " + str( value ) + " " )[value is not None]
simple: true
argpos: 1
mandatory: true
name: sequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2977']
- !mobyle/inputprogramparagraph
prompt: Options
name: options
argpos: 2
children:
- !mobyle/inputprogramparameter
comment: 'You can choose between:- blunt : Use blunt cutters- cohesive
: Use cohesive cutters- klenow : Use only 5'' enzymes for Klenow
fill-in.[Default all three]'
prompt: Type of enzymes (-T)
format: ( "" , " -T " + str( value ) )[value != vdef]
simple: true
name: enztype
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: blunt + cohesive + klenow, value: '0'}
- {label: blunt, value: blunt}
- {label: cohesive, value: cohesive}
- {label: klenow, value: klenow}
- !mobyle/inputprogramparameter
comment: 'Cohesive enzyme strand to use:- 5''- 3''- both : 5'' and 3''
(Default value).(No effect if you choose to use blunt enzymes)'
prompt: Cohesive enzyme strand (-S)
format: ( "" , " -S " + str( value ) )[value != vdef]
simple: true
name: strand
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: 5' + 3', value: '0'}
- {label: 5', value: '5'}
- {label: 3', value: '3'}
- !mobyle/inputprogramparameter
comment: 'Digestion mode:- double: Report couple of enzymes that digest
sequence- simple: Report enzyme name that cut more than one time-
both: simple + double (Default value).'
prompt: Digestion mode (-D)
format: ( "" , " -D " + str( value ) )[value != vdef]
simple: true
name: digestionmod
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: simple + double, value: '0'}
- {label: double, value: double}
- {label: simple, value: simple}
- !mobyle/inputprogramparameter
comment: Use enzymes with minimum length for DNA recognition site.By default,
6.
prompt: Minimum length of recognition site (-L)
format: ( "" , " -L " + str( value ) )[value is not None and value!=vdef]
name: Length
command: false
type: !mobyle/integertype {default: 6}
- !mobyle/inputprogramparameter
comment: Some cohesive enzymes have variant recognition site like 'GDGCH^C'
for Bsp1286I, where:D = not C (A or G or T)H = not G (A or C or T)This
option, when set, use of these type of enzymes..By default, this option
is off.
prompt: Use enzymes with variant recognition site (-V)
format: ( "" , " -V " )[value]
name: variant
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "Some cohesive enzymes have variant recognition site like 'GDGCH^C'\
\ for Bsp1286I, where:D = not C (A or G or T)H = not G (A or C or\
\ T)Thus, using thoses enzymes may produce a cut in frame but the\
\ produced ends may not be \n compatible together regarding\
\ DNA sequence.Requires the '[-V | --variant]' option to work. By\
\ default, this option is off."
prompt: Report digestions in frame without ends compatibilities (-X)
format: ( "" , " -X " )[value]
name: exotic
precond: {variant: '1'}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter {comment: 'File with list of compatible cohesive
ends.The default list used is given in the program help pages (compatible_cohesive_ends.txt).If
you want to give your own list, the format must be as follow:"Enzyme_name:compatEnz1_name,compatEnz2_name,..."',
prompt: List of compatible cohesive ends (-C), format: '( "" , " -C "
+ str( value ) )[value is not None]', name: compat, command: false}
- !mobyle/inputprogramparameter {comment: "By default, the program works with\
\ a list of enzymes commonly used in laboratory \n \t\tgiven\
\ in the program help pages (paillasse_liste.txt).If you want to give\
\ your own list, the format is one enzyme per line.", prompt: Enzyme
list to work with (-E), format: '( "" , " -E " + str( value ) )[value
is not None]', name: enzlist, command: false}
- !mobyle/inputprogramparagraph
prompt: Output parameters
name: outputopt
argpos: 3
children:
- !mobyle/inputprogramparameter
comment: "Sometimes, blunt digestion, after linkage, can produce new codon\
\ around the cutting site \n that leads to stop codon.This\
\ option displays such digestions with a tag 'stopCodon' in the output\
\ line results.NOTE: This option only works if 'blunt' type is set.\
\ By default this option is off, thus \n if such case happened\
\ no results are reported for enzymes digestion."
prompt: Show stop codon (-P)
format: ( "" , " -P " )[value]
name: stop
precond:
'#or':
- {enztype: '0'}
- {enztype: blunt}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "Enzymes may cut your sequence more than once.This option \n\
\ reports the number of time enzyme(s) cut your sequence.\
\ [Default off]"
prompt: Show cut positions (-N)
format: ( "" , " -N " )[value]
simple: true
name: cut_pos
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "Experimental option. [Default off]This option allows, for 'blunt'\
\ or 'klenow' analysis to\n show, in such case, the Amino\
\ acid that have been changed due to the ligation between \n \
\ the 2 parts of the DNA after the digestion.It will be shown\
\ as OldAA>NewAA (e.g.: G>N)."
prompt: Show new generated amino acid (-A)
format: ( "" , " -A " )[value]
name: mod_aa
precond:
enztype: {'#ne': cohesive}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: 'Choose the output type that you prefer.- Text output (Default
value)- GFF3 output- Image (png): Creates image (png).'
prompt: Output style format (-F)
format: ( "" , " -F " + str( value ) )[value != vdef]
simple: true
name: outputstyle
command: false
type: !mobyle/stringtype
default: text
options:
- {label: Text output, value: text}
- {label: GFF3 output, value: gff}
- {label: Image (png), value: image}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Output image
filenames: '"*.png"'
name: img
precond: {outputstyle: image}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"cif.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"cif.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
comment: "cif (for Cut In Frame) is a tool that works with DNA sequences. It is used\
\ to digest\n your sequences with a pool of restriction enzymes and to search\
\ which enzymes cut your\n sequence keeping your reading frame after ligation\
\ without any frame shift produced\n due to the digestion.This helps users\
\ to work with a gene of interest to localize potential region(s) that\n \
\ could be removed from the final protein to check if regions have an impact or\
\ not on\n the final gene product. It can also allow to identify vital region(s)\
\ for the gene."
operations: ['EDAM_operation:0431']
topics: ['EDAM_topic:0160']
documentation_links: ['http://bioweb2.pasteur.fr/docs/cif/cif.html', 'http://bioweb2.pasteur.fr/docs/cif/compatible_cohesive_ends.txt',
'http://bioweb2.pasteur.fr/docs/cif/paillasse_liste.txt']
command: cif
env: {}