mspurity_flagremove: spectralMatching.R comparison

comparison spectralMatching.R @ 11:7e4a5ce0877d draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3

author	tomnl
date	Thu, 27 Jun 2019 12:28:15 -0400
parents	6bd3ff77063c
children	2c8b5a640a04

comparison

equal deleted inserted replaced

-:b74303b60450
+:7e4a5ce0877d
 option_list <- list(
 make_option(c("-o", "--outDir"), type="character"),
 make_option("--q_dbPth", type="character"),
 make_option("--l_dbPth", type="character"),
 make_option("--q_msp", type="character", default=NA),
 make_option("--l_msp", type="character", default=NA),
 make_option("--q_defaultDb", action="store_true"),
 make_option("--l_defaultDb", action="store_true"),
 make_option("--q_ppmPrec", type="double"),
 make_option("--l_ppmPrec", type="double"),
 make_option("--q_ppmProd", type="double"),
 make_option("--l_ppmProd", type="double"),
 make_option("--q_raThres", type="double", default=NA),
 make_option("--l_raThres", type="double", default=NA),
 make_option("--q_polarity", type="character", default=NA),
 make_option("--l_polarity", type="character", default=NA),
 make_option("--q_purity", type="double", default=NA),
 make_option("--l_purity", type="double", default=NA),
 make_option("--q_xcmsGroups", type="character", default=NA),
 make_option("--l_xcmsGroups", type="character", default=NA),
 make_option("--q_pids", type="character", default=NA),
 make_option("--l_pids", type="character", default=NA),
 make_option("--q_rtrangeMin", type="double", default=NA),
 make_option("--l_rtrangeMin", type="double", default=NA),
 make_option("--q_rtrangeMax", type="double", default=NA),
 make_option("--l_rtrangeMax", type="double", default=NA),
 make_option("--q_accessions", type="character", default=NA),
 make_option("--l_accessions", type="character", default=NA),
 make_option("--q_sources", type="character", default=NA),
 make_option("--l_sources", type="character", default=NA),
 make_option("--q_sourcesUser", type="character", default=NA),
 make_option("--l_sourcesUser", type="character", default=NA),
 make_option("--q_instrumentTypes", type="character", default=NA),
 make_option("--l_instrumentTypes", type="character", default=NA),
 make_option("--q_instrumentTypesUser", type="character", default=NA),
 make_option("--l_instrumentTypesUser", type="character", default=NA),
 make_option("--q_instruments", type="character", default=NA),
 make_option("--l_instruments", type="character", default=NA),
 make_option("--q_spectraTypes", type="character", default=NA),
 make_option("--l_spectraTypes", type="character", default=NA),
 make_option("--q_spectraFilter", action="store_true"),
 make_option("--l_spectraFilter", action="store_true"),
 make_option("--usePrecursors", action="store_true"),
 make_option("--mzW", type="double"),
 make_option("--raW", type="double"),
 make_option("--rttol", type="double", default=NA),
 make_option("--updateDb", action="store_true"),
 make_option("--copyDb", action="store_true"),
 make_option("--cores", default=1)
 )
 # store options
 opt<- parse_args(OptionParser(option_list=option_list))
 param <- param[param != ""]
 }else{
 param <- NA
 }
 return(param)
 }
 if(!is.null(opt$q_defaultDb)){
 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
 }else if (!is.null(opt$q_dbPth)){
 sm <- msPurity::spectralMatching(q_dbPth = q_dbPth,
 l_dbPth = l_dbPth,
 q_purity =  opt$q_purity,
 l_purity =  opt$l_purity,
 q_ppmProd =  opt$q_ppmProd,
 l_ppmProd =  opt$l_ppmProd,
 q_ppmPrec =  opt$q_ppmPrec,
 l_ppmPrec =  opt$l_ppmPrec,
 q_raThres =  opt$q_raThres,
 l_raThres =  opt$l_raThres,
 q_pol =  q_polarity,
 l_pol =  l_polarity,
 q_xcmsGroups = q_xcmsGroups,
 l_xcmsGroups = l_xcmsGroups,
 q_pids = q_pids,
 l_pids = l_pids,
 q_sources = q_sources,
 l_sources = l_sources,
 q_instrumentTypes = q_instrumentTypes,
 l_instrumentTypes = l_instrumentTypes,
 q_spectraFilter= q_spectraFilter,
 l_spectraFilter= l_spectraFilter,
 l_rtrange=c(l_rtrangeMin, l_rtrangeMax),
 q_rtrange=c(q_rtrangeMin, q_rtrangeMax),
 q_accessions = opt$q_accessions,
 l_accessions= opt$l_accessions,
 raW = opt$raW,
 mzW = opt$mzW,
 rttol=opt$rttol,
 cores=opt$cores,
 copyDb=copyDb,
 updateDb=updateDb,
 outPth = "db_with_spectral_matching.sqlite"
 )
 q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){
 l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT  * FROM l_s_peak_meta')
 colnames(l_s_peak_meta)[1] <- 'pid'
 }
 l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth)
-if (DBI::dbExistsTable(q_con, "s_peaks")){
+if (DBI::dbExistsTable(l_con, "s_peaks")){
 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
-}else if(DBI::dbExistsTable(q_con, "library_spectra")){
+}else if(DBI::dbExistsTable(l_con, "library_spectra")){
-l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT  * FROM library_spectra
+l_s_peaks <- DBI::dbGetQuery(l_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")){
+if (DBI::dbExistsTable(l_con, "source")){
-l_source <- DBI::dbGetQuery(q_con, 'SELECT  * FROM source')
+l_source <- DBI::dbGetQuery(l_con, 'SELECT  * FROM source')
-}else if (DBI::dbExistsTable(q_con, "library_spectra_source")) {
+}else if (DBI::dbExistsTable(l_con, "library_spectra_source")) {
-l_source <- DBI::dbGetQuery(q_con, 'library_spectra_source')
+l_source <- DBI::dbGetQuery(l_con, 'SELECT  * FROM 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)
 }
 }

Mercurial > repos > tomnl > mspurity_flagremove

comparison spectralMatching.R @ 11:7e4a5ce0877d draft