R/app-quast.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# 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


ezMethodQuast = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
  opt = param$cmdOptions
  sampleName = input$getNames()
  draft = input$getFullPaths("Draft")
  if (ezIsSpecified(param$refGenome)){
  	ref = param$refGenome
	if (ezIsSpecified(param$refGene)){ 
    		gene = param$refGene
		cmd = paste("quast.py", "-R", ref, "-G", gene, "-o", sampleName, '-t', ezThreads(), opt, draft, "1> ", paste0(sampleName,"_quast.log"))
	}else{
		cmd = paste("quast.py", "-R", ref, "-o", sampleName, '-t', ezThreads(), opt, draft, "1> ", paste0(sampleName,"_quast.log"))
	}
  }else{
    	cmd = paste("quast.py", "-o", sampleName, '-t', ezThreads(), opt, draft, "1> ", paste0(sampleName,"_quast.log"))
  }
  ezSystem(cmd)
  return("Success")
}

##' @template app-template
##' @templateVar method ezMethodSpades()
##' @templateVar htmlArg )
##' @description Use this reference class to run 
EzAppQuast <-
  setRefClass("EzAppQuast",
              contains = "EzApp",
              methods = list(
                initialize = function()
                {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodQuast
                  name <<- "EzAppQuast"
		  appDefaults <<- rbind(refGenome = ezFrame(Type="character", DefaultValue="", Description="full path to a reference genome as a multi-fasta file"),
					refGene = ezFrame(Type="character", DefaultValue="",  Description="full path to a gene annotation file of the reference genome. Must be in gff or bed format"))

                }
              )
  )