diff sleuth.R @ 2:d6b5fc94062c draft default tip

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

--- a/sleuth.R	Wed Jun 07 11:47:30 2023 +0000
+++ b/sleuth.R	Thu Jun 08 19:57:53 2023 +0000
@@ -51,15 +51,11 @@
     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 = ""))
+
+  s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
+  for (f in args$factorLevel_counts) {
+    file.rename(f, paste(f, ".h5", sep = ""))
   }
-  for (f in paths) {
-    file.rename(f, gsub(".fastq.*", "", f))
-        file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
-  }
-  s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")
 
   so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
   so <- sleuth_fit(so)