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digest.yaml
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!mobyle/program
name: digest
title: digest
description: Reports on protein proteolytic enzyme or reagent cleavage sites
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Seqall option
format: ("", " -seqall=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: seqall
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:2976']
- !mobyle/inputprogramparameter {comment: Molecular weight data for amino
acids, prompt: Molecular weights data file, format: '("", " -mwdata="
+ str(value))[value is not None ]', argpos: 2, name: mwdata, command: false}
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
prompt: Enzymes and reagents
format: ("", " -menu=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: menu
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: Trypsin, value: '1'}
- {label: Lys-c, value: '2'}
- {label: Arg-c, value: '3'}
- {label: Asp-n, value: '4'}
- {label: V8-bicarb, value: '5'}
- {label: V8-phosph, value: '6'}
- {label: Chymotrypsin, value: '7'}
- {label: Cnbr, value: '8'}
- !mobyle/inputprogramparameter
prompt: Use monoisotopic weights
format: ("", " -mono")[ bool(value) ]
argpos: 4
name: mono
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Advanced section
name: advanced
children:
- !mobyle/inputprogramparameter
comment: Trypsin will not normally cut after 'KR' if they are followed
by any of 'KRIFLP'. Lys-C will not normally cut after 'K' if it
is followed by 'P'. Arg-C will not normally cut after 'R' if it
is followed by 'P'. V8-bicarb will not normally cut after 'E' if
it is followed by any of 'KREP'. V8-phosph will not normally cut
after 'DE' if they are followed by 'P'. Chymotrypsin will not normally
cut after 'FYWLM' if they are followed by 'P'. Specifying unfavoured
shows these unfavoured cuts as well as the favoured ones.
prompt: Allow unfavoured cuts
format: ("", " -unfavoured")[ bool(value) ]
argpos: 5
name: unfavoured
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Allows semi-specific and non-specific digestion. This option
is particularly useful for generating lists of peptide sequences
for protein identification using mass-spectrometry.
prompt: Allow ragging
format: ("", " -ragging")[ bool(value) ]
argpos: 6
name: ragging
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Ragging value (value from 1 to 4)
format: ("", " -termini=" + str(value))[value is not None and value!=vdef]
argpos: 7
name: termini
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: None, value: '1'}
- {label: Nterm, value: '2'}
- {label: Cterm, value: '3'}
- {label: Nterm or cterm, value: '4'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: Used for partial digestion. Shows all cuts from favoured cut
sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are
therefore fragments with exactly one potential cut site within it.
prompt: Show overlapping partials
format: ("", " -overlap")[ bool(value) ]
argpos: 8
name: overlap
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: As for overlap but fragments containing more than one potential cut
site are included.
prompt: Show all partials
format: ("", " -allpartials")[ bool(value) ]
argpos: 9
name: allpartials
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Name of the report file
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 10
name: outfile
command: false
type: !mobyle/stringtype {default: digest.report}
- !mobyle/inputprogramparameter
prompt: Choose the report output format
format: ("", " -rformat=" + str(value))[value is not None and value!=vdef]
argpos: 11
name: rformat_outfile
command: false
type: !mobyle/stringtype
default: SEQTABLE
options:
- {label: Dasgff, value: DASGFF}
- {label: Dbmotif, value: DBMOTIF}
- {label: Diffseq, value: DIFFSEQ}
- {label: Embl, value: EMBL}
- {label: Excel, value: EXCEL}
- {label: Feattable, value: FEATTABLE}
- {label: Genbank, value: GENBANK}
- {label: Gff, value: GFF}
- {label: Listfile, value: LISTFILE}
- {label: Motif, value: MOTIF}
- {label: Nametable, value: NAMETABLE}
- {label: Pir, value: PIR}
- {label: Regions, value: REGIONS}
- {label: Seqtable, value: SEQTABLE}
- {label: Simple, value: SIMPLE}
- {label: Srs, value: SRS}
- {label: Swiss, value: SWISS}
- {label: Table, value: TABLE}
- {label: Tagseq, value: TAGSEQ}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 12
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
precond:
rformat_outfile:
'#in': [DASGFF, DBMOTIF, DIFFSEQ, EMBL, EXCEL, FEATTABLE, GENBANK,
GFF, LISTFILE, MOTIF, NAMETABLE, PIR, REGIONS, SEQTABLE, SIMPLE,
SRS, SWISS, TABLE, TAGSEQ]
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"digest.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"digest.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0422']
topics: ['EDAM_topic:0141']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/digest.html', 'http://emboss.sourceforge.net/docs/themes']
command: digest
env: {}