blast
Basic Local Alignment Tool
Wraps BLAST [[Alt90]], probably the most popular similarity search tool in bioinformatics.
Commands
- clean
- Remove all job data, not the Moa job itself, note that this must be implemented by the template.
- report
- Generate a text BLAST report.
- run
- Running BLAST takes an input directory, determines what sequences are present and executes BLAST on each of these. Moa BLAST is configured to create XML output (as opposed to the standard text based output) in the out directory. The output XML is subsequently converted to GFF3 by the custom blast2gff script (using BioPython). Additionally, a simple text report is created.
Filesets
- db
Blast database
type: single
category: prerequisite
optional: False
pattern: */*
- input
- Directory with the input files for BLAST, in Fasta format
- outgff
GFF output files
type: map
source: input
category: output
optional: True
pattern: gff/*.gff
- output
XML blast output files
type: map
source: input
category: output
optional: True
pattern: out/*.out
Parameters
- eval
e value cutoff
type: float
default: 1e-10
optional: True
- gff_blasthit
(T,**F**) - export an extra blasthit feature to the created gff, grouping all hsp (match) features.
type: set
default: F
optional: True
- gff_source
source field to use in the gff
type: string
default: BLAST
optional: True
- nohits
number of hits to report
type: integer
default: 50
optional: True
- nothreads
threads to run blast with (note the overlap with the Make -j parameter)
type: integer
default: 2
optional: True
- program
blast program to use (default: blastn)
type: set
default: blastn
optional: True
miscellaneous
- Backend
- ruff
- Author
- Mark Fiers
- Creation date
- Wed Nov 10 07:56:48 2010
- Modification date
- Wed Nov 10 07:56:48 2010