blat

Blat

Run BLAT on an set of input files (query) vs a database.

Commands

clean

Remove all job data, not the Moa job itself, note that this must be implemented by the template.

run

no help defined

Parameters

db

type of the database (dna, prot or dnax)

type: set

default: ``

optional: False

db_id_list

a sorted list of db ids and descriptions, enhances the report generated

type: file

default: ``

optional: True

db_type

type of the database (dna, prot or dnax)

type: set

default: dna

optional: True

eval

evalue cutoff to select the reported hits on (defaults to 1e-15)

type: float

default: 1e-10

optional: True

gff_source

Source field for the generated GFF files

type: string

default: ``

optional: False

input_dir

source field in the generated gff

type: directory

default: ``

optional: False

input_extension

extension of the input files

type: string

default: fasta

optional: True

input_file

input query file. If this variable is not defined, the combination of blat_input_dir and blat_input_extension is used to find a list of input files

type: file

default: ``

optional: False

query_type

type of the query (dna, rna, prot, dnax or rnax)

type: set

default: dna

optional: True

miscellaneous

Backend

gnumake

Author

Mark Fiers

Creation date

Wed Nov 10 07:56:48 2010

Modification date

Wed Nov 10 07:56:48 2010