# HG changeset patch
# User tomnl
# Date 1525285606 14400
# Node ID 403ef9c5755042bd8918d38bbe092f268d7c05f8
# Parent  91f38a17d82a2cf425a83f667c67e131b8357043
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

diff -r 91f38a17d82a -r 403ef9c57550 anticipated_purity_dims.R
--- a/anticipated_purity_dims.R	Wed May 02 14:10:09 2018 -0400
+++ b/anticipated_purity_dims.R	Wed May 02 14:26:46 2018 -0400
@@ -42,7 +42,7 @@
 
   filename = sub("raw", "mzML", filename, ignore.case = TRUE)
   print(filename)
-  df <- indf[4:nrow(indf),]
+  df <- indf[3:nrow(indf),]
   if ('blank_flag' %in% colnames(df)){
     df <- df[df$blank_flag==1,]
   }
@@ -53,7 +53,7 @@
     df[df$mz=='nan',]$mz <- NA
   }
   df$mz <- as.numeric(df$mz)
-
+  mzml_file <- file.path(opt$mzML_file, filename)	
 
 
 
@@ -77,19 +77,6 @@
 }
 
 
-if (dir.exists(opt$mzML_file)){
-  # if directory then we need to add a file name
-  print(filename)
-  if (is.na(filename)){
-    print('ERROR: If a directory is provided then a filename needs to be entered
-          directory or automatically obtained by using a dimspy output')
-    quit()
-  }else{
-    mzml_file <- file.path(opt$mzML_file, filename)
-  }
-}else{
-  mzml_file <- opt$mzML_file
-}
 
 if (is.null(opt$sim)){
     sim=FALSE
@@ -118,7 +105,7 @@
 
 print('FIRST ROWS OF PEAK FILE')
 print(head(df))
-
+print(mzml_file)
 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                      filepth=mzml_file,
                                      minOffset=minOffset,