# HG changeset patch
# User tomnl
# Date 1525284720 14400
# Node ID b6d2cd8c54f033c0195c4ce882e416c872d33497
# Parent  b7f7ba5f52b50cbe00ba40bcfa76ea127f22f512
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

diff -r b7f7ba5f52b5 -r b6d2cd8c54f0 anticipated_purity_dims.R
--- a/anticipated_purity_dims.R	Wed May 02 13:19:15 2018 -0400
+++ b/anticipated_purity_dims.R	Wed May 02 14:12:00 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,]
   }