# HG changeset patch
# User workflow4metabolomics
# Date 1710430544 0
# Node ID 8242376d9f351004ddfb91f50a3919825248274c
# Parent 36480435e92bc29ce9edd99cf52f0fb649a184ad
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
diff -r 36480435e92b -r 8242376d9f35 abims_xcms_refine.xml
--- a/abims_xcms_refine.xml Mon Sep 11 09:21:15 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,264 +0,0 @@
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- Remove or merge chromatographic peaks based on specific criteria.
-
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- macros.xml
- macros_xcms.xml
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- 10.5281/zenodo.3909299
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- 10.1021/ac051437y
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diff -r 36480435e92b -r 8242376d9f35 abims_xcms_retcor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_xcms_retcor.xml Thu Mar 14 15:35:44 2024 +0000
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+ Retention Time Correction
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+ macros.xml
+ macros_xcms.xml
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diff -r 36480435e92b -r 8242376d9f35 xcms_refine.r
--- a/xcms_refine.r Mon Sep 11 09:21:15 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-#!/usr/bin/env Rscript
-
-# ----- LOG FILE -----
-log_file <- file("log.txt", open = "wt")
-sink(log_file)
-sink(log_file, type = "output")
-
-
-# ----- PACKAGE -----
-cat("\tSESSION INFO\n")
-
-#Import the different functions
-source_local <- function(fname) {
- argv <- commandArgs(trailingOnly = FALSE)
- base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
- source(paste(base_dir, fname, sep = "/"))
-}
-source_local("lib.r")
-
-pkgs <- c("xcms", "batch", "RColorBrewer")
-loadAndDisplayPackages(pkgs)
-cat("\n\n")
-
-# ----- ARGUMENTS -----
-cat("\tARGUMENTS INFO\n")
-# interpretation of arguments given in command line as an R list of objects
-args <- parseCommandArgs(evaluate = FALSE)
-write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
-
-cat("\n\n")
-
-# ----- PROCESSING INFILE -----
-cat("\tARGUMENTS PROCESSING INFO\n")
-
-#saving the specific parameters
-args_method <- args$method
-args_image <- args$image
-args_msLevel <- args$msLevel
-param_args <- list()
-
-if (args_method == "CleanPeaks") {
- param_args$maxPeakwidth <- args$maxPeakwidth
-} else if (args_method == "FilterIntensity") {
- param_args$threshold <- args$threshold
- param_args$value <- args$value
- param_args$nValues <- args$nValues
-} else if (args_method == "MergeNeighboringPeaks") {
- param_args$expandRt <- args$expandRt
- param_args$expandMz <- args$expandMz
- param_args$ppm <- args$ppm
- param_args$minProp <- args$minProp
-}
-
-cat("\n\n")
-
-
-# ----- ARGUMENTS PROCESSING -----
-cat("\tINFILE PROCESSING INFO\n")
-
-#image is an .RData file necessary to use xset variable given by previous tools
-load(args_image)
-if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
-
-# Handle infiles
-if (!exists("singlefile")) singlefile <- NULL
-if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
-
-cat("\n\n")
-
-
-# ----- MAIN PROCESSING INFO -----
-cat("\tMAIN PROCESSING INFO\n")
-
-
-cat("\t\tPREPARE PARAMETERS\n\n")
-
-if (args_method == "CleanPeaks") {
- refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
-} else if (args_method == "FilterIntensity") {
- refineChromPeaksParam <- FilterIntensityParam(
- threshold = param_args$threshold,
- nValues = param_args$nValues,
- value = param_args$value
- )
-} else if (args_method == "MergeNeighboringPeaks") {
- refineChromPeaksParam <- MergeNeighboringPeaksParam(
- expandRt = param_args$expandRt,
- expandMz = param_args$expandMz,
- ppm = param_args$ppm,
- minProp = param_args$minProp
- )
-}
-
-cat(str(refineChromPeaksParam))
-
-cat("\n\n\t\tCOMPUTE\n")
-
-xdata <- updateObject(xdata)
-
-xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
-
-cat("\n\n")
-
-# ----- EXPORT -----
-
-cat("\tXCMSnExp OBJECT INFO\n")
-print(xdata)
-cat("\n\n")
-
-cat("\txcmsSet OBJECT INFO\n")
-# Get the legacy xcmsSet object
-xset <- getxcmsSetObject(xdata)
-print(xset)
-cat("\n\n")
-
-#saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
-save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
-
-cat("\n\n")
-
-
-cat("\tDONE\n")
diff -r 36480435e92b -r 8242376d9f35 xcms_retcor.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_retcor.r Thu Mar 14 15:35:44 2024 +0000
@@ -0,0 +1,107 @@
+#!/usr/bin/env Rscript
+
+# ----- LOG FILE -----
+log_file <- file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+#Import the different functions
+source_local <- function(fname) {
+ argv <- commandArgs(trailingOnly = FALSE)
+ base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+ source(paste(base_dir, fname, sep = "/"))
+}
+source_local("lib.r")
+
+pkgs <- c("xcms", "batch", "RColorBrewer")
+loadAndDisplayPackages(pkgs)
+cat("\n\n")
+
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
+
+cat("\n\n")
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the specific parameters
+method <- args$method
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+args$image <- NULL
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+cat("\t\t\tAlignment/Retention Time correction\n")
+# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
+args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
+
+adjustRtimeParam <- do.call(paste0(method, "Param"), args)
+print(adjustRtimeParam)
+
+if (hasAdjustedRtime(xdata)) {
+ cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+ cat("Replace raw retention times with adjusted retention times.\n")
+ xdata <- applyAdjustedRtime(xdata)
+}
+xdata <- adjustRtime(xdata, param = adjustRtimeParam)
+
+cat("\n\n")
+
+
+# -- TIC --
+cat("\t\tDRAW GRAPHICS\n")
+getPlotAdjustedRtime(xdata)
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+print(xset)
+cat("\n\n")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")