diff combineAnnotations.R @ 15:70257c77ea04 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc

--- a/combineAnnotations.R	Fri Sep 27 09:19:17 2019 -0400
+++ b/combineAnnotations.R	Wed Nov 27 12:34:20 2019 +0000
@@ -14,15 +14,15 @@
   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("--sm_weight", type="numeric"),
+  make_option("--metfrag_weight", type="numeric"),
+  make_option("--sirius_csi_weight", type="numeric"),
+  make_option("--probmetab_weight", type="numeric"),
+  make_option("--ms1_lookup_weight", type="numeric"),
+  make_option("--biosim_weight", type="numeric"),
 
   make_option("--create_new_database", action="store_true"),
-  make_option(c("-o","--outdir"),type="character", default="."),
+  make_option("--outdir", type="character", default="."),
 
   make_option("--compoundDbType", type="character", default="sqlite"),
   make_option("--compoundDbPth", type="character", default=NA),
@@ -67,7 +67,8 @@
   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 = compoundDbType
+  compoundDbPth = opt$compoundDbPth
+  compoundDbType = opt$compoundDbType
   compoundDbName = NA
   compoundDbHost = NA
   compoundDbPort = NA