Mercurial > repos > tomnl > mspurity_createmsp

diff combineAnnotations.R @ 13:c43861c6924b draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4f88143938cc198436c2691443832c87e2c31cd0
author tomnl
date Tue, 24 Sep 2019 08:00:36 -0400
parents 5dd61e94d70d
children 70257c77ea04
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--- a/combineAnnotations.R	Fri Sep 13 11:53:46 2019 -0400
+++ b/combineAnnotations.R	Tue Sep 24 08:00:36 2019 -0400
@@ -67,7 +67,7 @@
   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
+  compoundDbType = compoundDbType
   compoundDbName = NA
   compoundDbHost = NA
   compoundDbPort = NA
@@ -79,7 +79,7 @@
 
 summary_output <- msPurity::combineAnnotations(
                             sm_resultPth = sm_resultPth,
-                            compoundDbPth = opt$compoundDbPth,
+                            compoundDbPth = compoundDbPth,
                             metfrag_resultPth = opt$metfrag_resultPth,
                             sirius_csi_resultPth = opt$sirius_csi_resultPth,
                             probmetab_resultPth = opt$probmetab_resultPth,