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diffseq.yaml
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!mobyle/program
name: diffseq
title: diffseq
description: Compare and report features of two similar sequences
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Asequence option
format: ("", " -asequence=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: asequence
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
prompt: Bsequence option
format: ("", " -bsequence=" + str(value))[value is not None]
simple: true
argpos: 2
mandatory: true
name: bsequence
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/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
comment: The similar regions between the two sequences are found by creating
a hash table of 'wordsize'd subsequences. 10 is a reasonable default.
Making this value larger (20?) may speed up the program slightly,
but will mean that any two differences within 'wordsize' of each
other will be grouped as a single region of difference. This value
may be made smaller (4?) to improve the resolution of nearby differences,
but the program will go much slower.
prompt: Word size (value greater than or equal to 2)
format: ("", " -wordsize=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: wordsize
command: false
type: !mobyle/integertype {default: 10}
ctrls:
- message: Value greater than or equal to 2 is required
test:
value: {'#gte': '2'}
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
comment: Normally this program will find regions of identity that are
the length of the specified word-size or greater and will then report
the regions of difference between these matching regions. This works
well and is what most people want if they are working with long overlapping
nucleic acid sequences. You are usually not interested in the non-overlapping
ends of these sequences. If you have protein sequences or short RNA
sequences however, you will be interested in differences at the very
ends . It this option is set to be true then the differences at the
ends will also be reported.
prompt: Force reporting of differences at the start and end
format: ("", " -globaldifferences")[ bool(value) ]
argpos: 4
name: globaldifferences
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
prompt: Name of the report file
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 5
name: outfile
command: false
type: !mobyle/stringtype {default: diffseq.report}
- !mobyle/inputprogramparameter
prompt: Choose the report output format
format: ("", " -rformat=" + str(value))[value is not None and value!=vdef]
argpos: 6
name: rformat_outfile
command: false
type: !mobyle/stringtype
default: DIFFSEQ
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
comment: File for output of first sequence's features
prompt: Name of the output feature file (aoutfeat)
format: ("" , " -aoutfeat=" + str(value))[value is not None]
argpos: 7
name: aoutfeat
command: false
type: !mobyle/stringtype {default: diffseq.aoutfeat}
- !mobyle/inputprogramparameter
prompt: Choose the feature output format
format: ("", " -offormat=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: offormat_aoutfeat
command: false
type: !mobyle/stringtype
default: GFF
options:
- {label: Gff, value: GFF}
- {label: Embl, value: EMBL}
- {label: Swissprot, value: SWISSPROT}
- {label: Nbrf, value: NBRF}
- {label: Pir, value: PIR}
- !mobyle/inputprogramparameter
comment: File for output of second sequence's features
prompt: Name of the output feature file (boutfeat)
format: ("" , " -boutfeat=" + str(value))[value is not None]
argpos: 9
name: boutfeat
command: false
type: !mobyle/stringtype {default: diffseq.boutfeat}
- !mobyle/inputprogramparameter
prompt: Choose the feature output format
format: ("", " -offormat=" + str(value))[value is not None and value!=vdef]
argpos: 10
name: offormat_boutfeat
command: false
type: !mobyle/stringtype
default: GFF
options:
- {label: Gff, value: GFF}
- {label: Embl, value: EMBL}
- {label: Swissprot, value: SWISSPROT}
- {label: Nbrf, value: NBRF}
- {label: Pir, value: PIR}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 11
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: Aoutfeat_out option, filenames: aoutfeat,
name: aoutfeat_out}
- !mobyle/outputprogramparameter {prompt: Boutfeat_out option, filenames: boutfeat,
name: boutfeat_out}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"diffseq.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"diffseq.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0256']
topics: ['EDAM_topic:0160']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/diffseq.html', 'http://emboss.sourceforge.net/docs/themes']
command: diffseq
env: {}