comparison limma_voom.R @ 2:a330ddf43861 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa

1:76d01fe0ec36

normCounts <- as.character(argv[14])
factPath <- as.character(argv[15])
# Process factors
if (as.character(argv[16])=="None") {
    factorData <- read.table(factPath, header=TRUE, sep="\t")
    factors <- factorData[,-1]
}  else { 
    factorData <- list()
    for (i in 16:length(argv)) {
        newFact <- unlist(strsplit(as.character(argv[i]), split="::"))
        factorData <- rbind(factorData, newFact)

cata("<table border=\"1\" cellpadding=\"3\">\n")
cata("<tr>\n")
TableHeadItem("SampleID")
TableHeadItem(names(factors)[1]," (Primary Factor)")

for (i in names(factors)[2:length(names(factors))]) {
  TableHeadItem(i)
}
cata("</tr>\n")

for (i in 1:nrow(factors)) {
  cata("<tr>\n")
  TableHeadItem(row.names(factors)[i])
  for (j in 1:ncol(factors)) {

2:a330ddf43861

normCounts <- as.character(argv[14])
factPath <- as.character(argv[15])
# Process factors
if (as.character(argv[16])=="None") {
    factorData <- read.table(factPath, header=TRUE, sep="\t")
    factors <- factorData[,-1, drop=FALSE]
}  else { 
    factorData <- list()
    for (i in 16:length(argv)) {
        newFact <- unlist(strsplit(as.character(argv[i]), split="::"))
        factorData <- rbind(factorData, newFact)

cata("<table border=\"1\" cellpadding=\"3\">\n")
cata("<tr>\n")
TableHeadItem("SampleID")
TableHeadItem(names(factors)[1]," (Primary Factor)")

  if (ncol(factors) > 1) {

    for (i in names(factors)[2:length(names(factors))]) {
      TableHeadItem(i)
    }
    cata("</tr>\n")
  }

for (i in 1:nrow(factors)) {
  cata("<tr>\n")
  TableHeadItem(row.names(factors)[i])
  for (j in 1:ncol(factors)) {