###################################################################
# 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
ezMethodPsortb = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
opt = param$cmdOptions
org = param$org
sampleName = input$getNames()
proteins = input$getFullPaths("Proteins")
ezSystem(paste("mkdir", sampleName))
cmd = paste("/usr/local/ngseq/src/psortb/psortb_app -i", proteins, "-r", sampleName, org, "--output terse", "-s /usr/local/ngseq/src/psortb/psortb.sif", opt, "1>", paste0(sampleName,"_psortb.log"))
ezSystem(cmd)
wddir <- "."
outfile <- list.files(paste0(wddir, "/", sampleName), pattern="_psortb_.*\\.txt")
outfile <- file.path(wddir, sampleName, outfile)
ezSystem(paste("cp", outfile, basename(output$getColumn("PsortbOut"))))
# proteins <- list.files(paste0(wddir, "/", sampleName), pattern=".proteins")
# proteins <- file.path(wddir, sampleName, proteins)
# ezSystem(paste("cp", proteins, basename(output$getColumn("Proteins"))))
return("Success")
}
##' @template app-template
##' @templateVar method ezMethodPsortb
##' @description Use this reference class to run
EzAppPsortb <-
setRefClass("EzAppPsortb",
contains = "EzApp",
methods = list(
initialize = function() {
"Initializes the application using its specific defaults."
runMethod <<- ezMethodPsortb
name <<- "EzAppPsortb"
appDefaults <<- rbind(
org = ezFrame(Type="character", DefaultValue="--negative", Description="type of organism: gram negative/ gram positive bacteria or archea")
)
}
)
)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.