diff sleuth.R @ 3:2c3d294dbe42 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 4adb19064a6973121680119529444286c24c1ac1

--- a/sleuth.R	Thu Jun 08 19:57:53 2023 +0000
+++ b/sleuth.R	Mon Jun 02 21:31:22 2025 +0000
@@ -1,6 +1,7 @@
 library(sleuth,
-        quietly = TRUE,
-        warn.conflicts = FALSE)
+    quietly = TRUE,
+    warn.conflicts = FALSE
+)
 library(annotables, quietly = TRUE, warn.conflicts = FALSE)
 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
 library(tidyverse)
@@ -8,11 +9,11 @@
 
 # setup R error handling to go to stderr
 options(
-  show.error.messages = FALSE,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, FALSE)
-  }
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
 )
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
@@ -28,113 +29,123 @@
 
 parser$add_argument("--factorLevel", action = "append", required = FALSE)
 parser$add_argument("--factorLevel_counts",
-                    action = "append",
-                    required = FALSE)
-parser$add_argument("--factorLevel_n", action = "append",  required = FALSE)
-parser$add_argument("--cores",  type = "integer", required = FALSE)
+    action = "append",
+    required = FALSE
+)
+parser$add_argument("--factorLevel_n", action = "append", required = FALSE)
+parser$add_argument("--cores", type = "integer", required = FALSE)
 parser$add_argument("--normalize", action = "store_true", required = FALSE)
 parser$add_argument("--nbins", type = "integer", required = FALSE)
 parser$add_argument("--lwr", type = "numeric", required = FALSE)
 parser$add_argument("--upr", type = "numeric", required = FALSE)
 parser$add_argument("--metadata_file",
-                    action = "append",
-                    required = FALSE)
+    action = "append",
+    required = FALSE
+)
 parser$add_argument("--experiment_design", required = FALSE)
 
 args <- parser$parse_args()
 
 if (args$experiment_design == "complex") {
-  ## Complex experiment design
-  ############################
-
-  s2c  <-
-    read.table(file = args$metadata_file,
-               header = TRUE,
-               sep = "\t")
+    ## Complex experiment design
+    ############################
 
-  s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
-  for (f in args$factorLevel_counts) {
-    file.rename(f, paste(f, ".h5", sep = ""))
-  }
+    s2c <-
+        read.table(
+            file = args$metadata_file,
+            header = TRUE,
+            sep = "\t"
+        )
 
-  so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
-  so <- sleuth_fit(so)
+    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 {
-  ## Simple experiment design
-  ###########################
+    ## Simple experiment design
+    ###########################
 
-  conditions <- c()
-  for (x in seq_along(args$factorLevel)) {
-    temp <- append(conditions, rep(args$factorLevel[[x]]))
-    conditions <- temp
-  }
+    conditions <- c()
+    for (x in seq_along(args$factorLevel)) {
+        temp <- append(conditions, rep(args$factorLevel[[x]]))
+        conditions <- temp
+    }
 
-  sample_names <-
-    gsub(".fastq.+", "", basename(args$factorLevel_counts))
+    sample_names <-
+        gsub(".fastq.+", "", basename(args$factorLevel_counts))
 
-  design <-
-    data.frame(list(
-      sample = sample_names,
-      condition = conditions,
-      path = args$factorLevel_counts
-    ))
-  so <- sleuth_prep(design,
-                    cores = args$cores,
-                    normalize = args$normalize)
+    design <-
+        data.frame(list(
+            sample = sample_names,
+            condition = conditions,
+            path = args$factorLevel_counts
+        ))
+    so <- sleuth_prep(design,
+        cores = args$cores,
+        normalize = args$normalize
+    )
 }
 
 so <- sleuth_fit(
-  so,
-  ~ condition,
-  "full",
-  n_bins = args$nbins,
-  lwr = args$lwr,
-  upr = args$upr
+    so,
+    ~condition,
+    "full",
+    n_bins = args$nbins,
+    lwr = args$lwr,
+    upr = args$upr
 )
 
 so <- sleuth_fit(
-  so,
-  ~ 1,
-  "reduced",
-  n_bins = args$nbins,
-  lwr = args$lwr,
-  upr = args$upr
+    so,
+    ~1,
+    "reduced",
+    n_bins = args$nbins,
+    lwr = args$lwr,
+    upr = args$upr
 )
 
 so <- sleuth_lrt(so, "reduced", "full")
 
 sleuth_table <-
-  sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
+    sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
 
 write.table(
-  sleuth_table,
-  file = "sleuth_table.tab",
-  quote = FALSE,
-  sep = "\t",
-  col.names = TRUE,
-  row.names = FALSE
+    sleuth_table,
+    file = "sleuth_table.tab",
+    quote = FALSE,
+    sep = "\t",
+    col.names = TRUE,
+    row.names = FALSE
 )
 
 
 outputFile <- file.path(getwd(), "pca_plot.pdf")
-pdf(file = outputFile,
+pdf(
+    file = outputFile,
     height = 6,
-    width = 9)
+    width = 9
+)
 plot_pca(so, color_by = "condition")
 dev.off()
 
 outputFile <- file.path(getwd(), "group_density.pdf")
-pdf(file = outputFile,
+pdf(
+    file = outputFile,
     height = 6,
-    width = 9)
+    width = 9
+)
 plot_group_density(
-  so,
-  use_filtered = TRUE,
-  units = "est_counts",
-  trans = "log",
-  grouping = setdiff(colnames(so$sample_to_covariates),
-                     "sample"),
-  offset = 1
+    so,
+    use_filtered = TRUE,
+    units = "est_counts",
+    trans = "log",
+    grouping = setdiff(
+        colnames(so$sample_to_covariates),
+        "sample"
+    ),
+    offset = 1
 )
 dev.off()