comparison sleuth.R @ 2:d6b5fc94062c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 10e44e324ee754d81a1b9d990ee0932b37e7a9bc

1:d3e447dd52c8

  s2c  <-
    read.table(file = args$metadata_file,
               header = TRUE,
               sep = "\t")
  paths <- c()
  for (x in s2c$data_filename) {
    paths <- c(paths, paste("./kallisto_outputs/",  x, sep = ""))
  }
  for (f in paths) {
    file.rename(f, gsub(".fastq.*", "", f))
        file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
  }
  s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")

  so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
  so <- sleuth_fit(so)

} else {

2:d6b5fc94062c

  s2c  <-
    read.table(file = args$metadata_file,
               header = TRUE,
               sep = "\t")

  s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
  for (f in args$factorLevel_counts) {
    file.rename(f, paste(f, ".h5", sep = ""))
  }

  so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
  so <- sleuth_fit(so)

} else {