# HG changeset patch
# User lecorguille
# Date 1536141561 14400
# Node ID 35a20d7c9f33c982b0dcedd917a04e93f6bb3de8
# Parent  e309e6af674434f81291a8f50a91123bd0d36ba7
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8

diff -r e309e6af6744 -r 35a20d7c9f33 abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Fri Aug 31 09:02:01 2018 -0400
+++ b/abims_xcms_retcor.xml	Wed Sep 05 05:59:21 2018 -0400
@@ -127,8 +127,8 @@
     </inputs>
 
     <outputs>
-        <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" from_work_dir="retcor.RData" />
-        <data name="rawVSadjustedPdf" format="pdf"  label="${image.name[:-6]}_rawVSadjusted.retcor.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
+        <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" />
+        <data name="rawVSadjustedPdf" format="pdf"  label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
     </outputs>
 
     <tests>
@@ -246,22 +246,22 @@
 
 **Upstream tools**
 
-========================= ================= ============================== ==========
-Name                      output file       format                         parameter
-========================= ================= ============================== ==========
-xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
-------------------------- ----------------- ------------------------------ ----------
-xcms.group                xset.group.RData  RData                          RData file
-========================= ================= ============================== ==========
+========================= ============================ ==============================
+Name                      Output file                  Format
+========================= ============================ ==============================
+xcms.findChromPeaks       raw.xset.RData               rdata.xcms.findchrompeaks
+------------------------- ---------------------------- ------------------------------
+xcms.groupChromPeaks      ``*``.groupChromPeaks.RData  rdata.xcms.group
+========================= ============================ ==============================
 
 
 **Downstream tools**
 
-=========================== ================== ========
-Name                        Output file        Format
-=========================== ================== ========
-xcms.group                  xset.retcor.RData  RData
-=========================== ================== ========
+=========================== ============================ ================
+Name                        Output file                  Format
+=========================== ============================ ================
+xcms.groupChromPeaks        ``*``.groupChromPeaks.RData  rdata.xcms.group
+=========================== ============================ ================
 
 
 **General schema of the metabolomic workflow**
@@ -296,9 +296,9 @@
 Output files
 ------------
 
-xset.group.retcor.RData: rdata.xcms.retcor format
+xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format
 
-    | Rdata file that will be necessary in the **xcms.group** step of the workflow.
+    | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.
 
 
 ---------------------------------------------------
diff -r e309e6af6744 -r 35a20d7c9f33 lib.r
--- a/lib.r	Fri Aug 31 09:02:01 2018 -0400
+++ b/lib.r	Wed Sep 05 05:59:21 2018 -0400
@@ -29,18 +29,21 @@
 
 #@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)
+mergeChrom <- function(chrom_merged, chrom) {
+    if (is.null(chrom_merged)) return(NULL)
+    chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
+    return(chrom_merged)
 }
 
 #@author G. Le Corguille
 # This function merge several xdata into one.
 mergeXData <- function(args) {
-    chromTIC <- NULL; chromBPI <- NULL
+    chromTIC <- NULL
+    chromBPI <- NULL
+    chromTIC_adjusted <- NULL
+    chromBPI_adjusted <- NULL
     for(image in args$images) {
+
         load(image)
         # Handle infiles
         if (!exists("singlefile")) singlefile <- NULL
@@ -49,9 +52,12 @@
         zipfile <- rawFilePath$zipfile
         singlefile <- rawFilePath$singlefile
         retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
         if (exists("raw_data")) xdata <- raw_data
         if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
         cat(sampleNamesList$sampleNamesOrigin,"\n")
+
         if (!exists("xdata_merged")) {
             xdata_merged <- xdata
             singlefile_merged <- singlefile
@@ -59,16 +65,21 @@
             sampleNamesList_merged <- sampleNamesList
             chromTIC_merged <- chromTIC
             chromBPI_merged <- chromBPI
+            chromTIC_adjusted_merged <- chromTIC_adjusted
+            chromBPI_adjusted_merged <- chromBPI_adjusted
         } else {
             if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
             else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
             else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
+
             singlefile_merged <- c(singlefile_merged,singlefile)
             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)
+            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
+            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
+            chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
+            chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
         }
     }
     rm(image)
@@ -76,8 +87,6 @@
     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")
@@ -92,7 +101,13 @@
             stop(error_message)
         }
     }
-    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
+
+    if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
+    if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
+    if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
+    if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
+
+    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
 }
 
 #@author G. Le Corguille
@@ -192,6 +207,9 @@
     return(myDataFrame)
 }
 
+#@author G. Le Corguille
+# Draw the BPI and TIC graphics
+# colored by sample names or class names
 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
 
     if (aggregationFun == "sum")
@@ -408,7 +426,7 @@
     for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
       singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
       singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
-      # In case, an url is used to import data within Galaxy 
+      # In case, an url is used to import data within Galaxy
       singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
       singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
     }
diff -r e309e6af6744 -r 35a20d7c9f33 static/images/xcms_retcor_workflow.png
Binary file static/images/xcms_retcor_workflow.png has changed