diff spectralMatching.R @ 0:cdf48fd76e98 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectralMatching.R	Fri May 24 09:04:36 2019 -0400
@@ -0,0 +1,245 @@
+library(msPurity)
+library(msPurityData)
+library(optparse)
+print(sessionInfo())
+
+
+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))
+
+print(opt)
+
+extractMultiple <- function(optParam){
+  if (!is.na(optParam)){
+     param <- trimws(strsplit(optParam, ',')[[1]])
+     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)){
+  q_dbPth <- opt$q_dbPth
+}else{
+  message('No query database available')
+  exit()
+}
+
+if(!is.null(opt$l_defaultDb)){
+  l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
+}else if (!is.null(opt$l_dbPth)){
+  l_dbPth <- opt$l_dbPth
+}else{
+  message('No library database available')
+  exit()
+}
+
+
+q_polarity <- extractMultiple(opt$q_polarity)
+l_polarity <- extractMultiple(opt$l_polarity)
+
+q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)
+l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)
+
+q_pids <- extractMultiple(opt$q_pids)
+l_pids <- extractMultiple(opt$l_pids)
+
+q_sources <- extractMultiple(opt$q_sources)
+l_sources <- extractMultiple(opt$l_sources)
+
+q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
+l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
+
+q_sources <-c(q_sources, q_sourcesUser)
+l_sources <-c(l_sources, l_sourcesUser)
+
+q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
+l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
+
+q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)
+l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)
+
+
+if(!is.null(opt$l_spectraFilter)){
+  l_spectraFilter <- TRUE
+}else{
+  l_spectraFilter <- FALSE
+}
+
+if(!is.null(opt$q_spectraFilter)){
+  q_spectraFilter <- TRUE
+}else{
+  q_spectraFilter <- FALSE
+}
+
+if(!is.null(opt$updateDb)){
+  updateDb <- TRUE
+}else{
+  updateDb <- FALSE
+}
+
+if(!is.null(opt$copyDb)){
+  copyDb <- TRUE
+}else{
+  copyDb <- FALSE
+}
+
+if(!is.null(opt$l_rtrangeMax)){
+  l_rtrangeMax <- opt$l_rtrangeMax
+}else{
+  l_rtrangeMax <- NA
+}
+
+if(!is.null(opt$q_rtrangeMax)){
+  q_rtrangeMax <- opt$q_rtrangeMax
+}else{
+  q_rtrangeMax <- NA
+}
+
+if(!is.null(opt$l_rtrangeMin)){
+  l_rtrangeMin <- opt$l_rtrangeMin
+}else{
+  l_rtrangeMin <- NA
+}
+
+if(!is.null(opt$q_rtrangeMin)){
+  q_rtrangeMin <- opt$q_rtrangeMin
+}else{
+  q_rtrangeMin <- NA
+}
+
+
+
+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"
+                           )
+
+
+
+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)