comparison create_sqlite_db.R @ 4:7ae48818a229 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a

3:3ecba7815437

  make_option("--cores", default=4),
  make_option("--mzML_files", type="character"),
  make_option("--galaxy_names", type="character"),
  make_option("--grp_peaklist", type="character"),
  make_option("--db_name", type="character", default='lcms_data.sqlite'),
  make_option("--raw_rt_columns", action="store_true")
)

# store options
opt<- parse_args(OptionParser(option_list=option_list))

loadRData <- function(rdata_path, name){

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

print('TESTETSTESTETE')
print(pa@fileList)


if (opt$xcms_camera_option=='xcms'){
  xset <- loadRData(opt$xset, 'xset')

  px <- msPurity::purityX(xset, saveEIC = TRUE,
                           cores=opt$cores, sqlitePth=db_pth,
                           rtrawColumns = rtrawColumns)
}



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

cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
             'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
             'FROM c_peak_groups AS cpg ',

4:7ae48818a229

  make_option("--cores", default=4),
  make_option("--mzML_files", type="character"),
  make_option("--galaxy_names", type="character"),
  make_option("--grp_peaklist", type="character"),
  make_option("--db_name", type="character", default='lcms_data.sqlite'),
  make_option("--raw_rt_columns", action="store_true"),
  make_option("--metfrag_result", type="character"),
  make_option("--sirius_csifingerid_result", type="character"),
  make_option("--probmetab_result", type="character")
)


# store options
opt<- parse_args(OptionParser(option_list=option_list))

loadRData <- function(rdata_path, name){

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


print(pa@fileList)


if (opt$xcms_camera_option=='xcms'){
  xset <- loadRData(opt$xset, 'xset')

  px <- msPurity::purityX(xset, saveEIC = TRUE,
                           cores=opt$cores, sqlitePth=db_pth,
                           rtrawColumns = rtrawColumns)
}

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

add_extra_table_elucidation <- function(name, pth){

  if (!is.null(pth)){
 
     print(pth)
     df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
     # 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)

  }

}


add_probmetab <- function(pth){
  if (!is.null(pth)){

      df <- read.table(pth,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
      df$grp_id <- 1:nrow(df)
      start <- T 
      for (i in 1:nrow(df)){

         x <- df[i,]


         if(is.na(x$proba) | x$proba =='NA'){

	   next
         }
  
         mpc <- stringr::str_split(x$mpc, ';')
         proba <- stringr::str_split(x$proba, ';') 

         for (j in 1:length(mpc[[1]])){
    
            row <-  c(x$grp_id, x$propmz, mpc[[1]][j], proba[[1]][j])
           
            if (start){
               df_out <- data.frame(t(row), stringsAsFactors=F)
               start <- F
            }else{
               df_out <- data.frame(rbind(df_out, row), stringsAsFactors=F)
            }
            print(df_out)

         } 
          
     }

     colnames(df_out) <- c('grp_id', 'propmz', 'mpc', 'proba')
     DBI::dbWriteTable(con, name='probmetab_results', value=df_out, row.names=FALSE)

  }


}

add_extra_table_elucidation('metfrag_results', opt$metfrag_result)
add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result)
add_probmetab(opt$probmetab_result)




cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
             'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
             'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
             'FROM c_peak_groups AS cpg ',