diff anticipated_purity_dims.R @ 9:cc4464eb380f draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

--- a/anticipated_purity_dims.R	Wed May 02 14:17:22 2018 -0400
+++ b/anticipated_purity_dims.R	Wed May 02 14:33:43 2018 -0400
@@ -53,7 +53,7 @@
     df[df$mz=='nan',]$mz <- NA
   }
   df$mz <- as.numeric(df$mz)
-
+  mzml_file <- file.path(opt$mzML_file, filename)	
 
 
 
@@ -77,20 +77,6 @@
 }
 
 
-if (dir.exists(opt$mzML_file)){
-  # if directory then we need to add a file name
-  print(filename)
-  if (is.na(filename)){
-    print('ERROR: If a directory is provided then a filename needs to be entered
-          directory or automatically obtained by using a dimspy output')
-    quit()
-  }else{
-    print('filename derived from dimspy')
-    mzml_file <- file.path(opt$mzML_file, filename)
-  }
-}else{
-  mzml_file <- opt$mzML_file
-}
 
 if (is.null(opt$sim)){
     sim=FALSE