comparison create_sqlite_db.R @ 14:69d5cb5a8e90 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535-dirty

13:4acad02faf32

db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
                          grp_peaklist=grp_peaklist, db_name=opt$db_name)

print(db_pth)

if (!is.null(opt$eic)){
  if (is.null(opt$raw_rt_columns)){
    rtrawColumns <- FALSE

  # 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,
                           cores=opt$cores, sqlitePth=db_pth,
                           rtrawColumns = rtrawColumns)
}

con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)

14:69d5cb5a8e90

db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
                          grp_peaklist=grp_peaklist, db_name=opt$db_name)
DBI::dbDisconnect()
print(db_pth)

if (!is.null(opt$eic)){
  if (is.null(opt$raw_rt_columns)){
    rtrawColumns <- FALSE

  # 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,
                           cores=1, sqlitePth=db_pth,
                           rtrawColumns = rtrawColumns)
}

con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)