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comparison sleuth.R @ 2:d6b5fc94062c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 10e44e324ee754d81a1b9d990ee0932b37e7a9bc
author iuc
date Thu, 08 Jun 2023 19:57:53 +0000
parents d3e447dd52c8
children 2c3d294dbe42
comparison
equal deleted inserted replaced
1:d3e447dd52c8 2:d6b5fc94062c
49 49
50 s2c <- 50 s2c <-
51 read.table(file = args$metadata_file, 51 read.table(file = args$metadata_file,
52 header = TRUE, 52 header = TRUE,
53 sep = "\t") 53 sep = "\t")
54 paths <- c() 54
55 for (x in s2c$data_filename) { 55 s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
56 paths <- c(paths, paste("./kallisto_outputs/", x, sep = "")) 56 for (f in args$factorLevel_counts) {
57 file.rename(f, paste(f, ".h5", sep = ""))
57 } 58 }
58 for (f in paths) {
59 file.rename(f, gsub(".fastq.*", "", f))
60 file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
61 }
62 s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")
63 59
64 so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1) 60 so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
65 so <- sleuth_fit(so) 61 so <- sleuth_fit(so)
66 62
67 } else { 63 } else {