Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

changeset 7:7399b23db662 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 08 Jun 2016 15:53:39 -0400
parents c922df2f9c2a
children f4badf0bf23a
files data_manager/customProDB_annotation.R
diffstat 1 files changed, 11 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/customProDB_annotation.R	Tue May 31 13:02:29 2016 -0400
+++ b/data_manager/customProDB_annotation.R	Wed Jun 08 15:53:39 2016 -0400
@@ -49,14 +49,18 @@
     {
         dbsnp = NULL
     }
-    
-    if (length(cosmic) > 0 && cosmic && grepl("^hg", dbkey))
+
+    use_cosmic = NULL
+    if (length(cosmic) > 0)
     {
-        use_cosmic = TRUE
-    }
-    else
-    {
-        use_cosmic = NULL
+        if (grepl("^hg", dbkey))
+        {
+            use_cosmic = TRUE
+        }
+        else
+        {
+            gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)")
+        }
     }
 
     suppressPackageStartupMessages(library(rjson))