diff spectral_matching.R @ 0:fe7d7cc95ca5 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectral_matching.R	Tue Mar 27 06:03:50 2018 -0400
@@ -0,0 +1,95 @@
+library(msPurity)
+library(optparse)
+
+option_list <- list(
+  make_option(c("-o", "--out_dir"), type="character"),
+  make_option("--target_db_pth", type="character"),
+  make_option("--library_db_pth", type="character"),
+  make_option("--ra_thres_l", default=0),
+  make_option("--ra_thres_t", default=2),
+  make_option("--cores", default=1),
+  make_option("--pol", default='positive'),
+  make_option("--ppm_tol_prod", default=10),
+  make_option("--ppm_tol_prec", default=5),
+  make_option("--score_thres", default=0.6),
+  make_option("--instrument_types", type='character'),
+  make_option("--library_sources", type='character'),
+  make_option("--scan_ids", default=NA),
+  make_option("--topn", default=NA),
+  make_option("--mzML_files", type="character"),
+  make_option("--galaxy_names", type="character"),
+  make_option("--create_new_database", action="store_true")
+
+)
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+
+
+if (!is.null(opt$create_new_database)){
+    target_db_pth <-  file.path(opt$out_dir, 'db_with_spectral_matching.sqlite')
+    file.copy(opt$target_db_pth, target_db_pth)
+}else{
+    target_db_pth <- opt$target_db_pth
+}
+
+
+if (opt$instrument_types=='None'){
+    instrument_types <- NA
+}else{
+    instrument_types <- trimws(strsplit(opt$instrument_types, ',')[[1]])
+}
+if (opt$library_sources=='None'){
+    library_sources <- NA
+}else{
+    library_sources <- trimws(strsplit(opt$library_sources, ',')[[1]])
+}
+
+
+if (!is.na(opt$scan_ids)){
+    scan_ids <- trimws(strsplit(opt$scan_ids, ',')[[1]])
+    scan_ids <- scan_ids[scan_ids != ""]
+}else{
+    scan_ids <- NA
+}
+
+
+print(instrument_types)
+print(library_sources)
+print(scan_ids)
+
+result <- msPurity::spectral_matching(
+                            target_db_pth =target_db_pth ,
+                            library_db_pth = opt$library_db_pth,
+                            ra_thres_l = opt$ra_thres_l,
+                            ra_thres_t = opt$ra_thres_t,
+                            cores = opt$cores,
+                            pol = opt$pol,
+                            ppm_tol_prod = opt$ppm_tol_prod,
+                            ppm_tol_prec = opt$ppm_tol_prec,
+                            score_thres = opt$score_thres,
+                            out_dir = opt$out_dir,
+                            topn = opt$topn,
+                            grp_peaklist = NA,
+
+                            instrument_types = instrument_types,
+                            library_sources = library_sources,
+                            scan_ids = scan_ids)
+
+print(file.path(result$result_db_pth))
+
+write.table(result$xcms_summary_df, file.path(opt$out_dir, 'xcms_hits.tsv'), row.names=FALSE, sep='\t')
+
+con <- DBI::dbConnect(RSQLite::SQLite(), file.path(result$result_db_pth))
+# con <- DBI::dbConnect(RSQLite::SQLite(), file.path(opt$out_dir, 'result.sqlite'))
+
+cmd <- paste('SELECT * FROM matches
+              LEFT JOIN library_meta ON matches.lid=library_meta.lid
+              LEFT JOIN s_peak_meta ON matches.pid=s_peak_meta.pid
+              LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid
+              WHERE matches.score >= ', opt$score_thres)
+print(cmd)
+scan_hits <- DBI::dbGetQuery(con, cmd)
+
+write.table(scan_hits, file.path(opt$out_dir, 'scan_hits.tsv'), row.names=FALSE, sep='\t')
\ No newline at end of file