diff ReadFids_wrapper.R @ 7:122df1bf0a8c draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995

--- a/ReadFids_wrapper.R	Wed May 13 03:52:09 2020 -0400
+++ b/ReadFids_wrapper.R	Fri Jul 11 08:33:38 2025 +0000
@@ -1,158 +1,97 @@
-#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
-
-## 08122016_ReadFids_wrapper.R
-## Manon Martin
-## [e-mail]
-
-##======================================================
-##======================================================
-# Preamble
-##======================================================
-##======================================================
-
-runExampleL <- FALSE
+## ------------------------------
+## Libraries laoding
+## ------------------------------
+# library(batch)
+library(optparse) # argument parsing
 
 
-##------------------------------
-## Options
-##------------------------------
-strAsFacL <- options()$stringsAsFactors
-options(stringsAsFactors = FALSE)
-options(warn=1)
-
-##------------------------------
-## Libraries laoding
-##------------------------------
-library(batch) 
-library(ggplot2)
-library(gridExtra)
-library(reshape2)
-
+## Outputs
+dataMatrix <- "dataMatrix.tsv"
+sampleMetadata <- "sampleMetadata.tsv"
+nomGraphe <- "graphOut.pdf"
+logOut <- "logOut.txt"
+sink(logOut, append = TRUE, split = TRUE)
 
-# R script call
-source_local <- function(fname)
-{
-  argv <- commandArgs(trailingOnly = FALSE)
-  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
-  source(paste(base_dir, fname, sep="/"))
-}
-#Import the different functions
-source_local("ReadFids_script.R")
-source_local("DrawFunctions.R")
-##------------------------------
-## Errors ?????????????????????
-##------------------------------
+# ------------------------------
+# Command line interface (optparse)
+# ------------------------------
+option_list <- list(
+    make_option(c("-f", "--fidzipfile"), type = "character", help = "Path to zipped Bruker FID file"),
+    make_option(c("-t", "--title_line"), type = "character", help = "Title line for output"),
+    make_option(c("-s", "--subdirectories"), action = "store_true", dest = "subdirectories", default = FALSE, help = "Whether to use subdirectories (boolean flag)"),
+    make_option(c("-d", "--dirs_names"), action = "store_true", dest = "dirs_names", default = FALSE, help = "Whether to use dirs_names (boolean flag)")
+)
 
-
-##------------------------------
-## Constants
-##------------------------------
-topEnvC <- environment()
-flagC <- "\n"
+opt_parser <- OptionParser(option_list = option_list)
+args <- parse_args(opt_parser)
+print(args)
 
 
-##------------------------------
-## Script
-##------------------------------
-if(!runExampleL)
-  argLs <- parseCommandArgs(evaluate=FALSE)
-
-sink(argLs$logOut)
-
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 ## Parameters Loading
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 
-	## Inputs
-		# Path
-			## Bruker FIDs
-fileType="Bruker"
-zipfile= argLs[["fidzipfile"]]
-directory=unzip(zipfile, list=F)
-path=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
-
+## Inputs
+# Path
+## Bruker FIDs
+fileType <- "Bruker"
+zipfile <- args$fidzipfile
+directory <- unzip(zipfile, list = FALSE)
+path <- paste(getwd(), strsplit(directory[1], "/")[[1]][2], sep = "/")
+print(path)
 
 # other inputs from ReadFids
-l = argLs[["title_line"]]
-subdirs <- argLs[["subdirectories"]]
-dirs.names <- argLs[["dirs_names"]]
-
-
-# Outputs
-# dataMatrix <- argLs[["dataMatrix"]]
-# sampleMetadata <- argLs[["sampleMetadata"]]
-logOut <- argLs[["logOut"]]
-nomGraphe <- argLs[["graphOut"]]
-	
+l <- args$title_line
+subdirs <- args$subdirectories
+dirs.names <- args$dirs_names
 
 
-## Checking arguments
-##-------------------
-error.stock <- "\n"
-
-if(length(error.stock) > 1)
-  stop(error.stock)
-
-
-
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 ## Computation
-##======================================================
-##======================================================
-sink(logOut,append=TRUE)
-
-if(length(warnings())>0){ # or !is.null(warnings())
-  print("something happened")
+## ======================================================
+## ======================================================
+if (length(warnings()) > 0) { # or !is.null(warnings())
+    print("something happened")
 }
 
 ## Starting
 cat("\nStart of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), "\n\n", sep = "")
 
-outputs <- ReadFids(path = path, l=l, subdirs = subdirs, dirs.names = dirs.names) 
-
+outputs <- ReadFids(path = path, l = l, subdirs = subdirs, dirs.names = dirs.names)
 data_matrix <- outputs[["Fid_data"]] # Data matrix
 data_sample <- outputs[["Fid_info"]] # Sample metadata
 
-
-
 pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
-title = "Raw FID data"
-DrawSignal(data_matrix, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
-             xlab = "Frequency", num.stacked = 4,
-             main = title, createWindow=FALSE)
+DrawSignal(data_matrix,
+    subtype = "stacked",
+    ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+    xlab = "Frequency", num.stacked = 4,
+    main = "Raw FID data", createWindow = FALSE
+)
 invisible(dev.off())
 
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 ## Saving
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 
 # Data matrix
-write.table(data_matrix,file=argLs$dataMatrix, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
+write.table(data_matrix, file = dataMatrix, quote = FALSE, row.names = TRUE, sep = "\t", col.names = TRUE)
 
 # Sample metadata
-write.table(data_sample,file=argLs$sampleMetadata, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
-
-# log file
-# write.table(t(data.frame(argLs)), file = argLs$logOut, col.names = FALSE, quote=FALSE)
+write.table(data_sample, file = sampleMetadata, quote = FALSE, row.names = TRUE, sep = "\t", col.names = TRUE)
 
 # input arguments
 cat("\n INPUT and OUTPUT ARGUMENTS :\n")
 
-argLs
-
+# Reproductibility
+print(sessionInfo())
 ## Ending
 
 cat("\nEnd of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), sep = "")
 
 sink()
-
-
-options(stringsAsFactors = strAsFacL)
-
-rm(list = ls())
\ No newline at end of file