Mercurial > repos > tomnl > assess_purity_msms

diff create_sqlite_db.R @ 17:52da05f657e1 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f396d6689e17cb5537f54ada02a6bd691c7894d7
author tomnl
date Tue, 15 May 2018 06:49:57 -0400
parents 96741e29cfd6
children 9fca32b9f106
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--- a/create_sqlite_db.R	Sun May 13 13:03:55 2018 -0400
+++ b/create_sqlite_db.R	Tue May 15 06:49:57 2018 -0400
@@ -124,6 +124,9 @@
   }else{
     rtrawColumns <- TRUE
   }
+  if (is.null(xset)){
+      xset <- xsa@xa
+  }
   # previous check should have matched filelists together
   xset@filepaths <- unname(pa@fileList)
 
@@ -146,7 +149,7 @@
 
      # get peakid, an scan id
      df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
-     colnames(df_ids) <- c('grp_id', 'file_id', 'peak_id')
+     colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
      df <- cbind(df_ids, df)
      # export to database