Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

changeset 8:f4badf0bf23a 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 16:00:30 -0400
parents 7399b23db662
children 9fec6c7f46eb
files data_manager/customProDB_annotation.R
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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())