###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch
ezMethodProkka = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
opt = param$cmdOptions
sampleName = input$getNames()
draft = input$getFullPaths("Draft")
cmd = paste("prokka --outdir", sampleName, "--prefix", sampleName, "--locustag", sampleName, "--compliant --centre FGCZ", "--kingdom", param$kingdom, "--cpus", ezThreads(), opt, draft, "1>", paste0(sampleName,"_prokka.log"))
ezSystem(cmd)
return("Success")
}
##' @template app-template
##' @templateVar method ezMethodProkka
##' @description Use this reference class to run
##' @seealso \code{\link{getPbmm2Reference}}
EzAppProkka <-
setRefClass("EzAppProkka",
contains = "EzApp",
methods = list(
initialize = function() {
"Initializes the application using its specific defaults."
runMethod <<- ezMethodProkka
name <<- "EzAppProkka"
appDefaults <<- rbind(
kingdom = ezFrame(Type="character", DefaultValue="Bacteria", Description="annotation mode and genetic code. Default is Bacteria")
)
}
)
)
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