getorf

Getorf

Predicts open reading frames using the EMBOSS [[emboss]] getorf tool.

Commands

clean

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

run

no help defined

Filesets

gff

type: map

source: input

category: output

optional: {}

pattern: ./gff/*.gff

input

Input files for getorf

output

type: map

source: input

category: output

optional: {}

pattern: ./out/*.out

Parameters

circular

Is the sequence linear?

type: set

default: N

optional: True

find

What to output? 0: Translation between stop codons, 1: Translation between start & stop codon, 2: Nucleotide sequence between stop codons; 3: Nucleotide sequence between start and stop codons. Default: 3

type: set

default: 3

optional: True

gff_source

source field to use in the gff.

type: string

default: getorf

optional: True

maxsize

maximal nucleotide size of the predicted ORF.

type: integer

default: 1000000

optional: True

minsize

minimal nucleotide size of the predicted ORF.

type: integer

default: 30

optional: True

table

Genetic code to use: 0 Standard; 1 Standard with alternative initiation codons; 2 Vertebrate Mitochondrial; 3 Yeast Mitochondrial; 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma; 5 Invertebrate Mitochondrial; 6 Ciliate Macronuclear and Dasycladacean; 9 Echinoderm Mitochondrial; 10 Euplotid Nuclear; 11 Bacterial; 12 Alternative Yeast Nuclear; 13 Ascidian Mitochondrial; 14 Flatworm Mitochondrial; 15 Blepharisma Macronuclear; 16 Chlorophycean Mitochondrial; 21 Trematode Mitochondrial; 22 Scenedesmus obliquus; 23 Thraustochytrium Mitochondrial.

type: set

default: 11

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