comparison create_sqlite_db.R @ 16:03e7f58e580e draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f396d6689e17cb5537f54ada02a6bd691c7894d7

15:cf24c8ca7a57

  if (is.null(opt$raw_rt_columns)){
    rtrawColumns <- FALSE
  }else{
    rtrawColumns <- TRUE
  }
  # previous check should have matched filelists together
  xset@filepaths <- unname(pa@fileList)

  # Saves the EICS into the previously created database
  px <- msPurity::purityX(xset, saveEIC = TRUE,

     # bug for repeating headers
     df <- df[!df$UID=='UID',]

     # get peakid, an scan id
     df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
     colnames(df_ids) <- c('grp_id', 'file_id', 'peak_id')
     df <- cbind(df_ids, df)
     # export to database
     

     DBI::dbWriteTable(con, name=name, value=df, row.names=FALSE)

16:03e7f58e580e

  if (is.null(opt$raw_rt_columns)){
    rtrawColumns <- FALSE
  }else{
    rtrawColumns <- TRUE
  }
  if (is.null(xset)){
      xset <- xsa@xa
  }
  # previous check should have matched filelists together
  xset@filepaths <- unname(pa@fileList)

  # Saves the EICS into the previously created database
  px <- msPurity::purityX(xset, saveEIC = TRUE,

     # bug for repeating headers
     df <- df[!df$UID=='UID',]

     # get peakid, an scan id
     df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
     colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
     df <- cbind(df_ids, df)
     # export to database
     

     DBI::dbWriteTable(con, name=name, value=df, row.names=FALSE)