diff anticipated_purity_dims.R @ 8:f6996ad60d8f draft

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

--- a/anticipated_purity_dims.R	Wed May 02 13:24:26 2018 -0400
+++ b/anticipated_purity_dims.R	Wed May 02 14:17:22 2018 -0400
@@ -32,16 +32,17 @@
 }else{
   indf <- read.table(opt$peaks_file,
                      header = TRUE, sep='\t', stringsAsFactors = FALSE)
-
+	
   filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
+  print(filename)
   # check if the data file is mzML or RAW (can only use mzML currently) so
   # we expect an mzML file of the same name in the same folder
   indf$i <- indf[,colnames(indf)==filename]
   indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
 
   filename = sub("raw", "mzML", filename, ignore.case = TRUE)
-
-  df <- indf[4:nrow(indf),]
+  print(filename)
+  df <- indf[3:nrow(indf),]
   if ('blank_flag' %in% colnames(df)){
     df <- df[df$blank_flag==1,]
   }
@@ -84,6 +85,7 @@
           directory or automatically obtained by using a dimspy output')
     quit()
   }else{
+    print('filename derived from dimspy')
     mzml_file <- file.path(opt$mzML_file, filename)
   }
 }else{
@@ -117,7 +119,7 @@
 
 print('FIRST ROWS OF PEAK FILE')
 print(head(df))
-
+print(mzml_file)
 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                      filepth=mzml_file,
                                      minOffset=minOffset,