changeset 3:59c1f9077c3b draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db

--- a/flagRemove.R	Fri Jun 14 06:55:56 2019 -0400
+++ b/flagRemove.R	Fri Jun 14 08:55:15 2019 -0400
@@ -71,11 +71,9 @@
               help="Assign True if files for each step saved (for testing purposes) [default = %default]"
   ),
 
-  make_option("--samplelist",  type="character", help="Sample list to determine the blank class"),
+  make_option("--samplelist",  type="character", help="Sample list to determine the blank class")
 
-  make_option("--xset_name",  default="xset",
-              help="Name of the xcmsSet object within the RData file [default = %default]"
-  )
+
 
 
 
@@ -108,13 +106,28 @@
 
 print(opt)
 
-loadRData <- function(rdata_path, xset_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)
+    }
+}
+
+
+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() == xset_name]))
+    return(get(ls()[ls() %in% name]))
 }
 
-xset<-loadRData(opt$xset_path, opt$xset_name)
+xset <- loadRData(opt$xset_path, c('xset','xdata'))
+
 print(xset)
 if (is.null(opt$samplelist)){
     blank_class <- opt$blank_class

--- a/flagRemove.xml	Fri Jun 14 06:55:56 2019 -0400
+++ b/flagRemove.xml	Fri Jun 14 08:55:15 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="mspurity_flagremove" name="msPurity.flagRemove" version="0.2.1">
+<tool id="mspurity_flagremove" name="msPurity.flagRemove" version="0.2.2">
     <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
         (e.g. RSD of intensity and retention time).
     </description>