comparison spectralMatching.R @ 8:c34cdaca2fcb draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 74e7bfbb5e70ec6e665114fa9e9863dafd7bced5

7:a3a969a82106

write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)

8:c34cdaca2fcb

write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)


# Add extra details from library spectra in resulting database
# First get all the ids from the l_s_peak_meta from the query database
if(updateDb){
  message('Adding extra details to database')
  q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
  if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){
    l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT  * FROM l_s_peak_meta')
    colnames(l_s_peak_meta)[1] <- 'pid'
  }
  
  l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth)
  if (DBI::dbExistsTable(q_con, "s_peaks")){
    l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
    
  }else if(DBI::dbExistsTable(q_con, "library_spectra")){
    l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM library_spectra 
                                                WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
  }else{
    l_s_peaks = NULL
  }
  
  if (DBI::dbExistsTable(q_con, "source")){
    l_source <- DBI::dbGetQuery(q_con, 'SELECT  * FROM source')
  }else if (DBI::dbExistsTable(q_con, "library_spectra_source")) {
    l_source <- DBI::dbGetQuery(q_con, 'library_spectra_source')
  }else{
    l_source = NULL
  }
  
  if (!is.null(l_s_peaks)){
    DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE)
  }
  
  if (!is.null(l_source)){
    DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE)
  }
  
}