diff xcms_xcmsSet.r @ 31:eb15a3841da4 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"

--- a/xcms_xcmsSet.r	Wed Feb 12 08:30:58 2020 -0500
+++ b/xcms_xcmsSet.r	Tue Apr 28 09:35:10 2020 -0400
@@ -40,6 +40,7 @@
 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
+if (!is.null(args$peaklist)) peaklistParam <- args$peaklist
 
 method <- args$method
 
@@ -100,6 +101,14 @@
 #chromTIC = chromatogram(xdata, aggregationFun = "sum")
 #chromBPI = chromatogram(xdata, aggregationFun = "max")
 
+# Create a chromPeaks table if required
+if (exists("peaklistParam")) {
+    if(peaklistParam){
+      cat("\nCreating the chromatographic peaks' table...\n")
+      write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F)
+	}
+}
+
 cat("\n\n")
 
 # ----- EXPORT -----