comparison create_sqlite_db.R @ 25:7bff866f72b5 draft

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

24:1e4eee6b7b93

print(sessionInfo())
print('CREATING DATABASE')


xset_pa_filename_fix <- function(opt, pa, xset){


  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 
    # needs to be done due to Galaxy moving the files around and screwing up any links to files

    }else{
      xset@filepaths <- unname(pa@fileList)
    }
  }


  return(list(pa, xset))
}

  return(get(ls()[ls() == name]))
}

print(paste('pa', opt$pa))
print(opt$xset)
print(opt$xcms_camera_option)
# Requires
pa <- loadRData(opt$pa, 'pa')

  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)

25:7bff866f72b5

print(sessionInfo())
print('CREATING DATABASE')


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 
    # needs to be done due to Galaxy moving the files around and screwing up any links to files

    }else{
      xset@filepaths <- unname(pa@fileList)
    }
  }


print(xset@phenoData)
print(xset@filepaths)

  return(list(pa, xset))
}

  return(get(ls()[ls() == name]))
}

print(paste('pa', opt$pa))
print(opt$xset)

print(opt$xcms_camera_option)
# Requires
pa <- loadRData(opt$pa, 'pa')

  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)