comparison create_sqlite_db.R @ 13:c7dd031d02b9 draft

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

12:291c9c7f63da

  }


  return(list(pa, xset))
}



option_list <- list(
  make_option(c("-o", "--out_dir"), type="character"),

}else{
  grp_peaklist = opt$grp_peaklist
}


print(pa@fileList)
print(xset@filepaths)


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


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

  # Saves the EICS into the previously created database
  px <- msPurity::purityX(xset, saveEIC = TRUE,
                           cores=opt$cores, sqlitePth=db_pth,
                           rtrawColumns = rtrawColumns)

13:c7dd031d02b9

  }


  return(list(pa, xset))
}




option_list <- list(
  make_option(c("-o", "--out_dir"), type="character"),

}else{
  grp_peaklist = opt$grp_peaklist
}





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