Nothing
RAxML <- function(file.name, file.path="", type="DNA", out.name=NULL,
model=NULL, bootstrap=NULL, algorithm="d", rseed=NULL,
args=NULL, numcat=25, nprocs=12, job.name=NULL,
print.curl=FALSE, shared.username=NULL, small=TRUE,
substitution.matrix=NULL, empirical.frequencies=FALSE,
suppress.Warnings=FALSE) {
type <- match.arg(type, c("DNA", "PROTEIN"))
if (type == "DNA"){
if (is.null(model)){
model="GTRCAT"
}
model <- match.arg(model, c("GTRCAT", "GTRGAMMA", "GTRCATI", "GTRGAMMAI"))
} else {
if (!is.null(substitution.matrix)){
substitution.matrix <- match.arg(substitution.matrix, c("DAYHOFF", "DCMUT", "JTT", "MTREV", "WAG", "RTREV", "CPREV", "VT", "BLOSUM62", "MTMAM", "LG", "MTART", "MTZOA", "PMB", "HIVB", "HIVW", "JTTDCMUT", "FLU", "GTR"))
}
if (is.null(model)){
if (empirical.frequencies==FALSE){
if (is.null(substitution.matrix)){
model="PROTCATBLOSUM62"
other.models <- c("PROTCATBLOSUM62", "PROTGAMMABLOSUM62", "PROTCATIBLOSUM62", "PROTGAMMAIBLOSUM62")
} else {
model=paste("PROTCAT", substitution.matrix, sep="")
other.models <- c(paste("PROTCAT", substitution.matrix, sep=""), paste("PROTGAMMA", substitution.matrix, sep=""), paste("PROTCATI", substitution.matrix, sep=""), paste("PROTGAMMAI", substitution.matrix, sep=""))
}
} else {
if (is.null(substitution.matrix)){
model="PROTCATBLOSUM62F"
other.models <- c("PROTCATBLOSUM62F", "PROTGAMMABLOSUM62F", "PROTCATIBLOSUM62F", "PROTGAMMAIBLOSUM62F")
} else {
model=paste("PROTCAT", substitution.matrix, "F", sep="")
other.models <- c(paste("PROTCAT", substitution.matrix, "F", sep=""), paste("PROTGAMMA", substitution.matrix, "F", sep=""), paste("PROTCATI", substitution.matrix, "F", sep=""), paste("PROTGAMMAI", substitution.matrix, "F", sep=""))
}
}
} else {
if (empirical.frequencies==FALSE){
if (is.null(substitution.matrix)){
model=paste(model, "BLOSUM62", sep="")
other.models <- c("PROTCATBLOSUM62", "PROTGAMMABLOSUM62", "PROTCATIBLOSUM62", "PROTGAMMAIBLOSUM62")
} else {
model=paste(model, substitution.matrix, sep="")
other.models <- c(paste("PROTCAT", substitution.matrix, sep=""), paste("PROTGAMMA", substitution.matrix, sep=""), paste("PROTCATI", substitution.matrix, sep=""), paste("PROTGAMMAI", substitution.matrix, sep=""))
}
} else {
if (is.null(substitution.matrix)){
model=paste(model, "BLOSUM62F", sep="")
other.models <- c("PROTCATBLOSUM62F", "PROTGAMMABLOSUM62F", "PROTCATIBLOSUM62F", "PROTGAMMAIBLOSUM62F")
} else {
model=paste(model, substitution.matrix, "F", sep="")
other.models <- c(paste("PROTCAT", substitution.matrix, "F", sep=""), paste("PROTGAMMA", substitution.matrix, "F", sep=""), paste("PROTCATI", substitution.matrix, "F", sep=""), paste("PROTGAMMAI", substitution.matrix, "F", sep=""))
}
}
}
model <- match.arg(model, other.models)
}
if (rplant.env$api == "a") {
if (small) {
version="RAxML-small-8.2.3u1"
} else {
version="RAxML-medium-8.2.3u1"
}
App <- GetAppInfo(version)[[3]]
input.list <- vector("list",1)
input.list[[1]] <- App[,2][1]
# input.list[[1]] <- "inname"
#initialize arguments
options <- c(args)
args <- NULL
args <- append(args, list(c("model", model)))
args <- append(args, list(c("N", 10)))
# args <- append(args, list(c("threads", nprocs)))
if (is.null(rseed)){
args <- append(args, list(c("p", 123456)))
} else {
args <- append(args, list(c("p", rseed)))
}
if (!is.null(out.name)){
args <- append(args, list(c("outname", out.name)))
} else {
args <- append(args, list(c("outname", "nwk")))
}
if (!is.null(bootstrap)) {
options <- append(options, c("-b", bootstrap))
}
options <- append(options, c("-f", algorithm))
#options <- append(options, c("-#", numberOfRuns))
options <- append(options, c("-c", numcat))
options <- paste(options, collapse=" ") # make a single statement
args <- append(args, list(c("options", options)))
} else {
version="raxml-lonestar-7.2.8u1"
App <- GetAppInfo(version)[[3]]
input.list <- vector("list",1)
input.list[[1]] <- App[,2][1]
#initialize arguments
args <- c(args)
args <- append(args, c("-m", model))
args <- append(args, c("-N", 10))
args <- append(args, c("-T", nprocs))
if (!is.null(bootstrap)) {
args <- append(args, c("-b", bootstrap))
}
args <- append(args, c("-f", algorithm))
if (is.null(rseed)){
args <- append(args, c("-p", floor(runif(1, 1, 10^6))))
} else {
args <- append(args, c("-p", rseed))
}
#args <- append(args, c("-#", numberOfRuns))
args <- append(args, c("-c", numcat))
if (!is.null(out.name)){
args <- append(args, c("-n", out.name))
} else {
args <- append(args, c("-n", "nwk"))
}
args <- paste(args, collapse=" ") # make a single statement
args <- list(c("arguments", args))
}
if (is.null(job.name)){
# job.name <- paste(rplant.env$user, "_RAxMLprotein_", model, "_viaR", sep="")
job.name <- version
}
# Submit
myJob<-SubmitJob(application=version, job.name=job.name, nprocs=nprocs,
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,
args.list=args)
return(myJob)
}
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