Nothing
Muscle <- function(file.name, file.path="", job.name=NULL, args=NULL,
aln.filetype="PHYLIP_INT", shared.username=NULL, out.name=NULL,
suppress.Warnings=FALSE, print.curl=FALSE) {
fm=NULL
aln.filetype <- match.arg(aln.filetype, c("PHYLIP_INT", "PHYLIP_SEQ", "HTML", "FASTA", "CLUSTALW", "MSF"))
if (rplant.env$api == "f") {
privAPP=FALSE
version="Muscle-3.8.32u4"
if (aln.filetype == "PHYLIP_INT"){
args <- append(args, "-phyiout")
aln.name <- "phylip_interleaved.aln"
} else if (aln.filetype == "PHYLIP_SEQ"){
args <- append(args, "-physout")
aln.name <- "phylip_sequential.aln"
} else if (aln.filetype == "FASTA"){
args <- append(args, "-fastaout")
aln.name <- "fasta.aln"
} else if (aln.filetype == "CLUSTALW"){
args <- append(args, "-clwout")
aln.name <- "clustalw.aln"
} else if (aln.filetype == "MSF"){
args <- append(args, "-msfout")
aln.name <- "msf.aln"
} else if (aln.filetype == "HTML"){
args <- append(args, "-htmlout")
aln.name <- "html.aln"
}
args <- paste(args, collapse=" ") # make a single statement
App <- GetAppInfo(version)[[3]]
input.list <- vector("list",1)
input.list[[1]] <- App[,2][1]
if (is.null(job.name))
job.name <- paste(rplant.env$user,"_",version,"_viaR", sep="")
args <- list(c("arguments",args))
} else {
version="Muscle-hpc-3.8.31u1"
if (aln.filetype == "PHYLIP_INT"){
fm <- append(fm, "-phyiout")
} else if (aln.filetype == "PHYLIP_SEQ"){
fm <- append(fm, "-physout")
} else if (aln.filetype == "FASTA"){
fm <- append(fm, "-fastaout")
} else if (aln.filetype == "CLUSTALW"){
fm <- append(fm, "-clwout")
} else if (aln.filetype == "MSF"){
fm <- append(fm, "-msfout")
} else if (aln.filetype == "HTML"){
fm <- append(fm, "-htmlout")
}
if (is.null(out.name)) {
if (aln.filetype == "PHYLIP_INT"){
out.name <- "phylip_interleaved.aln"
} else if (aln.filetype == "PHYLIP_SEQ"){
out.name <- "phylip_sequential.aln"
} else if (aln.filetype == "FASTA"){
out.name <- "fasta.aln"
} else if (aln.filetype == "CLUSTALW"){
out.name <- "clustalw2.aln"
} else if (aln.filetype == "MSF"){
out.name <- "msf.aln"
} else if (aln.filetype == "HTML"){
out.name <- "html.aln"
}
}
App <- GetAppInfo(version)[[3]]
input.list <- vector("list",1)
input.list[[1]] <- App[,2][1]
#Sinput.list[[1]] <- "stdin"
if (is.null(job.name)) {
# job.name <- paste(rplant.env$user,"_",version,"_viaR", sep="")
job.name <- version
}
if (!is.null(args)){
args <- paste(args, collapse=" ") # make a single statement
args <- list(c("format", fm), c("outname", out.name), c("arguments",args))
} else {
args <- list(c("format", fm), c("outname", out.name))
}
}
myJob<-SubmitJob(application=version, job.name=job.name, args.list=args,
file.list=list(file.name), file.path=file.path,
input.list=input.list, suppress.Warnings=suppress.Warnings,
print.curl=print.curl, shared.username=shared.username)
cat(paste("Result file: ", out.name, "\n", sep=""))
return(myJob)
}
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