megaptera (version 1.0-0)

megapteraProj: Bundle Input Data for the Pipeline

Description

Create an object of class megapteraProj to hold all the input data necessary for running of the pipeline.

Usage

megapteraProj(db, taxon, locus = locus(),  align.exe, mask.exe,  params = megapteraPars(),  update = FALSE, parallel = FALSE)

Arguments

db

an object of class dbPars.

taxon

an object of class taxon.

locus

an object of class locus.

align.exe

a vector of mode "character", giving name of the alignment program; currently only MAFFT is allowed

mask.exe

a vector of mode "character", giving name of the alignment masking program; currently only Gblocks is allowed

params

an object of class megapteraPars.

update

logical: if TRUE, the pipeline's steps are executed as if called fro the first time, i.e., possibly overriding data and setting that have been previously achieved.

parallel

logical: if TRUE, several step in the pipeline will be run in parallel, otherwise all steps are serial.

Value

an object of class megapteraProj

See Also

dbPars, taxon, locus, and megapteraPars for defining of database parameters, taxa, loci, and the pipeline's parameters, respectively.