diff create_sqlite_db.R @ 25:7bff866f72b5 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty

--- a/create_sqlite_db.R	Sat Jun 02 05:14:23 2018 -0400
+++ b/create_sqlite_db.R	Mon Jun 11 07:49:38 2018 -0400
@@ -7,7 +7,7 @@
 
 
 xset_pa_filename_fix <- function(opt, pa, xset){
-
+  print(xset@filepaths)
 
   if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
     # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables 
@@ -41,6 +41,9 @@
   }
 
 
+print(xset@phenoData)
+print(xset@filepaths)
+
   return(list(pa, xset))
 }
 
@@ -76,6 +79,7 @@
 
 print(paste('pa', opt$pa))
 print(opt$xset)
+
 print(opt$xcms_camera_option)
 # Requires
 pa <- loadRData(opt$pa, 'pa')
@@ -111,8 +115,6 @@
 
 
 
-
-
 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
                           grp_peaklist=grp_peaklist, db_name=opt$db_name)