# HG changeset patch
# User lecorguille
# Date 1522965887 14400
# Node ID fa17ee3bc9ce08351ae6ea29475ee9aa45f1a158
# Parent  efc5be79596f7de73e15bb3027ee5fce63822ae3
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty

diff -r efc5be79596f -r fa17ee3bc9ce lib.r
--- a/lib.r	Tue Apr 03 11:54:23 2018 -0400
+++ b/lib.r	Thu Apr 05 18:04:47 2018 -0400
@@ -28,8 +28,18 @@
 }
 
 #@author G. Le Corguille
+# This function merge several chromBPI or chromTIC into one.
+mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
+    if (is.null(chromTIC_merged)) return(NULL)
+    chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
+    chromTIC_merged@phenoData <- xdata_merged@phenoData
+    return(chromTIC_merged)
+}
+
+#@author G. Le Corguille
 # This function merge several xdata into one.
 mergeXData <- function(args) {
+    chromTIC <- NULL; chromBPI <- NULL
     for(image in args$images) {
         load(image)
         # Handle infiles
@@ -47,6 +57,8 @@
             singlefile_merged <- singlefile
             md5sumList_merged <- md5sumList
             sampleNamesList_merged <- sampleNamesList
+            chromTIC_merged <- chromTIC
+            chromBPI_merged <- chromBPI
         } else {
             if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
             else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
@@ -55,6 +67,8 @@
             md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
             sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
             sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
+            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
+            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
         }
     }
     rm(image)
@@ -62,6 +76,8 @@
     singlefile <- singlefile_merged; rm(singlefile_merged)
     md5sumList <- md5sumList_merged; rm(md5sumList_merged)
     sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
+    chromTIC <- chromTIC_merged; rm(chromTIC_merged)
+    chromBPI <- chromBPI_merged; rm(chromBPI_merged)
 
     if (!is.null(args$sampleMetadata)) {
         cat("\tXSET PHENODATA SETTING...\n")
@@ -76,7 +92,7 @@
             stop(error_message)
         }
     }
-    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
+    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
 }
 
 #@author G. Le Corguille
@@ -176,9 +192,8 @@
     return(myDataFrame)
 }
 
-getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
+getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
 
-    chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
     if (aggregationFun == "sum")
         type="Total Ion Chromatograms"
     else
@@ -207,16 +222,6 @@
     dev.off()
 }
 
-#@author G. Le Corguille
-getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
-    getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
-}
-
-#@author G. Le Corguille
-getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
-    getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
-}
-
 
 # Get the polarities from all the samples of a condition
 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
diff -r efc5be79596f -r fa17ee3bc9ce msnbase_readmsdata.r
--- a/msnbase_readmsdata.r	Tue Apr 03 11:54:23 2018 -0400
+++ b/msnbase_readmsdata.r	Thu Apr 05 18:04:47 2018 -0400
@@ -76,6 +76,10 @@
 # Create a sampleMetada file
 sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv")
 
+cat("\t\t\tCompute and Store TIC and BPI\n")
+chromTIC <- chromatogram(raw_data, aggregationFun = "sum")
+chromBPI <- chromatogram(raw_data, aggregationFun = "max")
+
 cat("\n\n")
 
 # ----- EXPORT -----
@@ -87,7 +91,7 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData")
 
 
diff -r efc5be79596f -r fa17ee3bc9ce msnbase_readmsdata.xml
--- a/msnbase_readmsdata.xml	Tue Apr 03 11:54:23 2018 -0400
+++ b/msnbase_readmsdata.xml	Thu Apr 05 18:04:47 2018 -0400
@@ -61,7 +61,7 @@
             </assert_stdout>
         </test>
         <!-- DISABLE FOR TRAVIS
-        Useful to generate test-data for the further steps
+        Useful to generate test-data for the further steps-->
         <test>
             <param name="input" value="ko16.CDF"  ftype="netcdf" />
             <assert_stdout>
@@ -86,7 +86,7 @@
                 <has_text text="./wt16.CDF        wt16            ." />
             </assert_stdout>
         </test>
-        -->
+        <!-- -->
     </tests>
 
     <help><![CDATA[
diff -r efc5be79596f -r fa17ee3bc9ce test-data/ko16.CDF
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diff -r efc5be79596f -r fa17ee3bc9ce test-data/wt15.CDF
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diff -r efc5be79596f -r fa17ee3bc9ce test-data/wt16.CDF
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