gmap¶

Gmap

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

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: no help defined

align

type: map

source: input

category: output

optional: {}

pattern: ./align/*.align

genepred

type: map

source: input

category: output

optional: {}

pattern: ./genepred/*.genepred

gff

type: map

source: input

category: output

optional: {}

pattern: ./gff/*.gff

gff_invert

type: map

source: input

category: output

optional: {}

pattern: ./gff/*.invert.gff

raw

type: map

source: input

category: output

optional: {}

pattern: ./raw/*.raw

db: Gmap db

type: file

default: ``

optional: False
extra_parameters: extra parameters to feed to gmap

type: string

default: ``

optional: True
gff_source: Source field to use in the output GFF

type: string

default: gmap

optional: True
invert_gff: Invert the GFF (T/F)

type: set

default: T

optional: True