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blast2genoclass_1.0.yaml
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blast2genoclass_1.0.yaml
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!mobyle/program
name: blast2genoclass
version: '1.0'
title: blast2genoclass
description: One-line description of Blast program filtering
authors: C. Maufrais
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
prompt: Blast output file
format: '" -i " + str(value)'
simple: true
argpos: 20
mandatory: true
name: infile
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:0857']
- !mobyle/inputprogramparameter
prompt: 'Filter the one-line description of Blast program with:'
format: ("", " -" + str(value))[value != vdef]
simple: true
name: blastfilter
command: false
type: !mobyle/stringtype
default: 'Null'
options:
- {label: null, value: 'Null'}
- {label: best e-value, value: M}
- {label: most frequent description, value: F}
- !mobyle/inputprogramparameter
comment: '0: all hsp'
prompt: Number of hsp to consider (-x)
format: ("", " -x " + str(value) )[value is not None and value != vdef]
name: nbofhit
command: false
type: !mobyle/integertype {default: 10}
- !mobyle/inputprogramparameter
prompt: Filter the one-line description of Blast program with user name (-p)
format: ("", " -p " + str(value).replace(' ','_') )[value is not None]
simple: true
name: genomic_name
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Filter the hit of Blast with Taxonomic hierarchy name (-n)
format: ("", " -n " + str(value).replace(' ','_') )[value is not None]
simple: true
mandatory: true
name: taxonomic_name
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Output option
name: output
children:
- !mobyle/inputprogramparameter
comment: 'In "res4individualBlast.txt" file, for all input blast, are
details:For all matching "Description filter option":- query name,
(query letter): percentage of matching descriptionand for all corresponding
hits:- Database sequence''s species, accession number and letters-
Hsp description'
prompt: Report detailed results matching "Description filter option" for
all blast (-v)
format: ("" , " -v") [value]
name: verboseall
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: In "res4allBlast.txt" file, for the best database sequence(s),
are details:For database sequence matching "Description filter option":-
Database sequence's species, accession number, letters and description-
Number of query matching this sequence.- Query name, (letters)and
for all corresponding hsp:- Hsp description
prompt: Detailed report for database sequence(s) matching "Description
filter option" (-V)
format: ("" , " -V") [value]
name: verbose
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Hsp(s) selection (-m)
format: ("", " -m " + str(value))[value != vdef]
name: option
command: false
type: !mobyle/stringtype
default: '1'
options:
- {label: All hsps, value: '0'}
- {label: Only compatible hsps, value: '1'}
- {label: Simple overlaps are possible, value: '2'}
- {label: Global overlaps on database sequence(s) are possible, value: '3'}
- !mobyle/inputprogramparameter
comment: For 1,2,3 hsps alignments (Sbjt and Query) are re-aligned on
the reference sequence extract from database.For 4,5,6 part of queries
corresponding to hsps are re-aligned on the reference sequence extract
from database.
prompt: 'Produce alignment: database sequence matching "Description filter
option" vs queries (-a)'
format: ("" , " -a " +str(value)) [value != vdef]
name: align
command: false
type: !mobyle/stringtype
default: '0'
options:
- {label: null, value: '0'}
- {label: 'hsps blast and database sequence reference alignment: hsp
merged in pairwise alignment', value: '1'}
- {label: 'hsps blast and database sequence reference alignment: hsp
in multiple alignment', value: '2'}
- {label: 'hsps blast and database sequence reference alignment: hsp
in multiple alignment and consensus', value: '3'}
- {label: 'part of queries (hsp) and database sequence reference alignment:
queries merged in pairwise alignment', value: '4'}
- {label: 'part of queries (hsp) and database sequence reference alignment:
queries in multiple alignment', value: '5'}
- {label: 'part of queries (hsp) and database sequence reference alignment:
queries in multiple alignment and consensus', value: '6'}
- !mobyle/inputprogramparameter
prompt: 'Produce graphical alignment summary images: database sequence
matching "Description filter option" vs queries (-g)'
format: ("" , " -g") [value]
name: picture
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Blast output file(s) sort/split by specific taxonomic hierarchy
(-b)
format: ("" , " -b") [value]
name: blastout
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Extract Hsp(s) fragment from Query sequence(s) (-Q)
format: ("" , " -Q") [value]
name: hspSeq
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Query name write in file(s) sort/split by specific taxonomic hierarchy
(-q)
format: ("" , " -q") [value]
name: queryout
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Report database sequence(s) matching option in fasta file (-s)
format: ("" , " -s") [value]
name: besthitseq
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Extract fasta sequence, matching specified taxonomic filter,
from file containing query sequences witch are used to made blast.
prompt: Extraction of fasta sequences.
name: fastaExtract
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Query sequences witch are used to made blast.
name: query_seq
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Query sequences witch are used to made blast.
format: (""," -f "+ str(query_seq)) [query_seq is not None]
name: query_seq_run1
precond:
'#and': [hspSeq, query_seq]
command: false
hidden: true
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Query sequences witch are used to made blast.
format: (""," && extractfasta -i "+ str(query_seq) + " *.qry") [query_seq
is not None]
argpos: 100
name: query_seq_run2
precond:
'#and': [fastaExtract, queryout, query_seq]
command: false
hidden: true
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output option
name: output
children:
- !mobyle/outputprogramparameter
prompt: Output file
filenames: '"blast2genoclass.out"'
name: outfile
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter {prompt: Graphical output, filenames: '"*.png"',
name: pictureout, precond: picture}
- !mobyle/outputprogramparameter
prompt: Alignment
filenames: '"*.aln"'
name: alignout
precond: align
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Verbose output file for all blast
filenames: '"res4individualBlast.txt"'
name: verboseoutall
precond: verboseall
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Verbose output file for database sequence(s)
filenames: '"res4allBlast.txt"'
name: verboseout
precond: verbose
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Blast output file(s)
filenames: '"*.blast"'
name: blastoutfile
precond: blastout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:0857']
- !mobyle/outputprogramparameter
prompt: Query name file
filenames: '"*.qry"'
name: queryoutfile
precond: queryout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Database sequence(s) fasta file
filenames: '"*.dbfasta"'
name: besthitseqfile
precond: besthitseq
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Fasta file
filenames: '"*.fasta"'
name: fastafile
precond:
'#or': [fastaExtract, hspSeq]
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200']
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"blast2genoclass.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0258']
topics: ['EDAM_topic:0182', 'EDAM_topic:0623']
command: blast2genoclass
env: {}