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changeset 9:cc4464eb380f draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 14:33:43 -0400
parents f6996ad60d8f
children cf82f99f3638
files anticipated_purity_dims.R
diffstat 1 files changed, 1 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- 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