glimmer3¶
Glimmer3
Predicts (prokaryotic) using glimmer3.
Commands¶
- clean
- Remove all job data, not the Moa job itself, note that this must be implemented by the template.
- run
- Glimmer3 is a open reading frame discovery program from the EMBOSS [[emboss]] package. It takes a set of input sequences and predicts all open reading frames. Additionally, this template converts the default output (predicted protein sequences) to GFF3.
Filesets¶
- cds
CDS output files from glimmer3
type: mapsource: inputcategory: outputoptional: Truepattern: cds/*.fasta- gff
GFF output files from glimmer3
type: mapsource: inputcategory: outputoptional: Truepattern: gff/*.gff- input
- Directory with the input files for Glimmer3
- output
Raw output files from glimmer3
type: mapsource: inputcategory: outputoptional: Truepattern: out/*.g3- pep
peptide output files from glimmer3
type: mapsource: inputcategory: outputoptional: Truepattern: pep/*.fasta
Parameters¶
- gene_len
Minimum gene length (glimmer3 -g/–gene_len)
type: integerdefault: 110optional: True- gff_source
source field to use in the gff. Defaults to “glimmer3”
type: stringdefault: glimmer3optional: True- max_overlap
Maximum overlap, see the glimmer documentation for the -o or –max_olap parameter
type: integerdefault: 50optional: True- stop_codons
stop codons
type: {}default: tag,tga,taa,nnn,tnn,ann,gnn,cnnoptional: True- treshold
treshold for calling a gene a gene (glimmer3 -t)
type: integerdefault: 30optional: 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