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blast2taxoclass_1.0.yaml
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blast2taxoclass_1.0.yaml
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!mobyle/program
name: blast2taxoclass
version: '1.0'
title: blast2taxoclass
description: Blast filtering with taxonomic hierarchy information
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: 'Find taxonomic classification of:'
format: '" -" + str(value)'
simple: true
name: blastfilter
command: false
type: !mobyle/stringtype
default: M
options:
- {label: best hit, value: M}
- {label: most frequent hit, 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
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/inputprogramparagraph
prompt: Taxonomic hierarchy filter option
name: taxonomicfilter
children:
- !mobyle/inputprogramparameter
comment: 'zero means: root of taxonomy, higher value: leaf or near'
prompt: Relative position in taxonomic hierarchy (-p)
format: ("", " -p " + str(value) )[value is not None]
simple: true
name: position
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Taxonomic Name (-n)
format: ("", " -n " + str(value).replace(' ','_') )[value is not None]
simple: true
name: taxonomic_name
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: If Taxonomic rank is not defined for one hit, it is not treated.
prompt: Taxonomic rank name (-r)
format: ("", " -r " + str(value) )[value is not None]
simple: true
name: rank
command: false
type: !mobyle/stringtype
default: 'null'
options:
- {label: null, value: 'null'}
- {label: superkingdom, value: superkingdom}
- {label: kingdom, value: kingdom}
- {label: subkingdom, value: subkingdom}
- {label: superphylum, value: superphylum}
- {label: phylum, value: phylum}
- {label: subphylum, value: subphylum}
- {label: superclass, value: superclass}
- {label: class, value: class}
- {label: subclass, value: subclass}
- {label: infraclass, value: infraclass}
- {label: superorder, value: superorder}
- {label: order, value: order}
- {label: suborder, value: suborder}
- {label: infraorder, value: infraorder}
- {label: parvorder, value: parvorder}
- {label: superfamily, value: superfamily}
- {label: family, value: family}
- {label: subfamily, value: subfamily}
- {label: tribe, value: tribe}
- {label: subtribe, value: subtribe}
- {label: genus, value: genus}
- {label: subgenus, value: subgenus}
- {label: species_group, value: species_group}
- {label: species_subgroup, value: species_subgroup}
- {label: species, value: species}
- {label: subspecies, value: subspecies}
- {label: varietas, value: varietas}
- {label: forma, value: forma}
- !mobyle/inputprogramparagraph
prompt: Output option
name: output
children:
- !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: 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
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.
format: (""," && extractfasta -i "+ str(value) + " *.qry") [value is not
None]
argpos: 100
name: query_seq
precond:
'#and': [fastaExtract, queryout]
command: false
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: '"blast2taxoclass.out"'
name: outfile
output_type: stdout
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: Fasta file
filenames: '"*.fasta"'
name: fastafile
precond: fastaExtract
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"blast2taxoclass.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0258', 'EDAM_operation:0637']
topics: ['EDAM_topic:0182', 'EDAM_topic:0637']
command: blast2taxoclass
env: {}