Mercurial > repos > computational-metabolomics > mspurity_spectralmatching

diff purityX.R @ 9:c33b92eeb1fb draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:37:41 +0000
parents 77706396e7bd
children fcd8ef711617
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--- a/purityX.R	Wed Jun 12 16:03:14 2024 +0000
+++ b/purityX.R	Thu Jun 13 11:37:41 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)
   }
 }