diff purityX.R @ 9:548fed2ef792 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f

--- a/purityX.R	Wed Jun 12 16:05:52 2024 +0000
+++ b/purityX.R	Thu Jun 13 11:40:06 2024 +0000
@@ -74,14 +74,18 @@
 
 getxcmsSetObject <- function(xobject) {
   # XCMS 1.x
-  if (class(xobject) == "xcmsSet") {
+  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$sample_group
+    if (!is.null(xset@phenoData$sample_group)){
+      xcms::sampclass(xset) <- xset@phenoData$sample_group
+    }else{
+      xcms::sampclass(xset) <- "."
+    }
     return(xset)
   }
 }