Squashed initial commit

qhtcp-workflow/apps/r/CompileGTF.R

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+#!/usr/bin/env Rscript
+
+# Load the openxlsx package
+library(openxlsx)
+
+args <- commandArgs(TRUE)
+
+outDir <- args[1]
+
+# Function to combine CSV and TXT files into a workbook with named sheets
+combineFilesToWorkbook <- function(file_list, output_file) {
+  # Create a new workbook
+  wb <- createWorkbook()
+  
+  # Loop through the file list
+  for (i in seq_along(file_list)) {
+    file <- file_list[i]
+    
+    # Extract the sheet name from the file name based on the extension
+    ext <- tools::file_ext(file)
+    sheet_name <- tools::file_path_sans_ext(basename(file))
+    
+    # Read the data based on the file extension
+    if (ext %in% c("csv", "txt")) {
+      if (ext == "csv") {
+        data <- read.csv(file)
+      } else if (ext == "txt") {
+        data <- readLines(file)
+      }
+      
+      # Create a new sheet in the workbook with the extracted sheet name
+      addWorksheet(wb, sheetName = sheet_name)
+      
+      # Write the data to the sheet
+      writeData(wb, sheet = sheet_name, x = data)
+    }
+  }
+  
+  # Save the workbook as an Excel file
+  saveWorkbook(wb, output_file)
+}
+
+Component <- file.path(outDir, "Component", "ComponentResults.txt")
+Function <- file.path(outDir, "Function", "FunctionResults.txt")
+Process <- file.path(outDir, "Process", "ProcessResults.txt")
+
+# Specify the list of input files (both CSV and TXT)
+file_list <- c(Component, Process, Function)
+
+# Specify the output file name
+output_file <- file.path(outDir, "GTFCombined.xlsx")
+
+# Call the function to combine the files into a workbook with named sheets
+combineFilesToWorkbook(file_list, output_file)