# HG changeset patch
# User galaxyp
# Date 1465416030 14400
# Node ID f4badf0bf23a04213fac28d2710b99308b1d24b6
# Parent  7399b23db662608cc04fb4e1a5a74ed1377f20f7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty

diff -r 7399b23db662 -r f4badf0bf23a data_manager/customProDB_annotation.R
--- a/data_manager/customProDB_annotation.R	Wed Jun 08 15:53:39 2016 -0400
+++ b/data_manager/customProDB_annotation.R	Wed Jun 08 16:00:30 2016 -0400
@@ -91,7 +91,7 @@
     download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
 
     cat(paste("Preparing Refseq annotation files\n"))
-    customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, cosmic=use_cosmic)
+    customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic)
     
     outputPath = paste(dbkey, "/customProDB", sep="")
     output = list(data_tables = list())