diff xcms_xcmsSet.r @ 33:c363b9f1caef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

--- a/xcms_xcmsSet.r	Thu Mar 01 04:14:39 2018 -0500
+++ b/xcms_xcmsSet.r	Mon Mar 05 04:15:34 2018 -0500
@@ -37,6 +37,16 @@
 register(BPPARAM)
 
 #saving the specific parameters
+if (!is.null(args$filterAcquisitionNum)){
+    filterAcquisitionNumParam <- args$filterAcquisitionNum; args$filterAcquisitionNum <- NULL
+}
+if (!is.null(args$filterRt)){
+    filterRtParam <- args$filterRt; args$filterRt <- NULL
+}
+if (!is.null(args$filterMz)){
+    filterMzParam <- args$filterMz; args$filterMz <- NULL
+}
+
 method <- args$method; args$method <- NULL
 
 cat("\n\n")
@@ -80,6 +90,17 @@
 cat("\t\t\tLoad Raw Data\n")
 raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk")
 
+cat("\t\t\tApply filter[s] (if asked)\n")
+if (exists("filterAcquisitionNumParam")) {
+    raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
+}
+if (exists("filterRtParam")) {
+    raw_data <- filterRt(raw_data, filterRtParam)
+}
+if (exists("filterMzParam")) {
+    raw_data <- filterMz(raw_data, filterMzParam)
+}
+
 cat("\t\t\tChromatographic peak detection\n")
 findChromPeaksParam <- do.call(paste0(method,"Param"), args)
 print(findChromPeaksParam)
@@ -90,7 +111,7 @@
 
 # Transform the files absolute pathways into relative pathways
 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
-save.image()
+
 # Create a sampleMetada file
 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")