diff combineAnnotations.R @ 11:a90832e6acb2 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea

--- a/combineAnnotations.R	Thu Jun 27 12:40:06 2019 -0400
+++ b/combineAnnotations.R	Fri Sep 13 11:57:28 2019 -0400
@@ -8,13 +8,25 @@
   make_option(c("-m","--metfrag_resultPth"),type="character"),
   make_option(c("-c","--sirius_csi_resultPth"),type="character"),
   make_option(c("-p","--probmetab_resultPth"),type="character"),
+  make_option(c("-l","--ms1_lookup_resultPth"),type="character"),
+
+  make_option("--ms1_lookup_checkAdducts", action="store_true"),
+  make_option("--ms1_lookup_keepAdducts", type="character", default=NA),
+  make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
+
   make_option(c("-sw","--sm_weight"),type="numeric"),
   make_option(c("-mw","--metfrag_weight"),type="numeric"),
   make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
   make_option(c("-pw","--probmetab_weight"),type="numeric"),
+  make_option(c("-lw","--ms1_lookup_weight"),type="numeric"),
+  make_option(c("-bw","--biosim_weight"),type="numeric"),
+
   make_option("--create_new_database", action="store_true"),
   make_option(c("-o","--outdir"),type="character", default="."),
-  make_option("--eic", action="store_true")
+
+  make_option("--compoundDbType", type="character", default="sqlite"),
+  make_option("--compoundDbPth", type="character", default=NA),
+  make_option("--compoundDbHost", type="character", default=NA)
 )
 opt <- parse_args(OptionParser(option_list=option_list))
 
@@ -27,23 +39,61 @@
   sm_resultPth <- opt$sm_resultPth
 }
 
+if (is.null(opt$ms1_lookup_checkAdducts)){
+  opt$ms1_lookup_checkAdducts <- FALSE
+}
+if (!is.null(opt$ms1_lookup_keepAdducts)){
+    opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
+    opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
+    ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
+}
 
 weights <-list('sm'=opt$sm_weight,
                'metfrag'=opt$metfrag_weight,
                'sirius_csifingerid'= opt$sirius_csi_weight,
-               'probmetab'=opt$probmetab_weight
+               'probmetab'=opt$probmetab_weight,
+               'ms1_lookup'=opt$ms1_lookup_weight,
+               'biosim'=opt$biosim_weight
                )
-
+print(weights)
 if (round(!sum(unlist(weights),0)==1)){
 
   stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
 }
 
-summary_output <- msPurity::combineAnnotations(sm_resultPth,
-                             opt$metfrag_resultPth,
-                             opt$sirius_csi_resultPth,
-                             opt$probmetab_resultPth,
-                             weights = weights)
+if (opt$compoundDbType=='local_config'){
+  # load in compound config
+  # Soure local function taken from workflow4metabolomics
+  source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+  source_local("dbconfig.R")
+}else{
+  compoundDbType = opt$compoundDbType
+  compoundDbName = NA
+  compoundDbHost = NA
+  compoundDbPort = NA
+  compoundDbUser = NA
+  compoundDbPass = NA
+}
+
+
+
+summary_output <- msPurity::combineAnnotations(
+                            sm_resultPth = sm_resultPth,
+                            compoundDbPth = opt$compoundDbPth,
+                            metfrag_resultPth = opt$metfrag_resultPth,
+                            sirius_csi_resultPth = opt$sirius_csi_resultPth,
+                            probmetab_resultPth = opt$probmetab_resultPth,
+                            ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
+                            ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
+                            ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
+
+                            compoundDbType = compoundDbType,
+                            compoundDbName = compoundDbName,
+                            compoundDbHost = compoundDbHost,
+                            compoundDbPort = compoundDbPort,
+                            compoundDbUser = compoundDbUser,
+                            compoundDbPass = compoundDbPass,
+                            weights = weights)
 
 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)