# HG changeset patch
# User tomnl
# Date 1560510012 14400
# Node ID 250599939950a2f8967a3e496d9e0f6cf3cb5700
# Parent  e4d251e0b7ebde10a8334423528d4e6a6b91e99d
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit d9efa3f24732a92c2bcef5987289179e86d5c50f-dirty

diff -r e4d251e0b7eb -r 250599939950 createDatabase.R
--- a/createDatabase.R	Tue Jun 04 10:50:35 2019 -0400
+++ b/createDatabase.R	Fri Jun 14 07:00:12 2019 -0400
@@ -68,11 +68,25 @@
 print(opt)
 
 loadRData <- function(rdata_path, name){
-  #loads an RData file, and returns the named xset object if it is there
-  load(rdata_path)
-  return(get(ls()[ls() == name]))
+#loads an RData file, and returns the named xset object if it is there
+    load(rdata_path)
+    return(get(ls()[ls() %in% name]))
 }
 
+getxcmsSetObject <- function(xobject) {
+    # XCMS 1.x
+    if (class(xobject) == "xcmsSet")
+        return (xobject)
+    # XCMS 3.x
+    if (class(xobject) == "XCMSnExp") {
+        # Get the legacy xcmsSet object
+        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        sampclass(xset) <- xset@phenoData$sample_group
+        return (xset)
+    }
+}
+
+
 print(paste('pa', opt$pa))
 print(opt$xset)
 
@@ -84,8 +98,11 @@
 print(pa@fileList)
 
 
+
 if (opt$xcms_camera_option=='xcms'){
-  xset <- loadRData(opt$xset, 'xset')
+  
+  xset <- loadRData(opt$xset, c('xset','xdata'))
+  xset <- getxcmsSetObject(xset)
   fix <- xset_pa_filename_fix(opt, pa, xset)  
   pa <- fix[[1]]
   xset <- fix[[2]]
@@ -111,9 +128,9 @@
 
 dbPth <- msPurity::createDatabase(pa,
                                    xset=xset,
-#                                   xsa=xa, 
+                                   xsa=xa, 
                                    outDir=opt$outDir,
-#                                   grpPeaklist=grpPeaklist,
+                                   grpPeaklist=grpPeaklist,
                                    dbName='createDatabase_output.sqlite'
 )