# HG changeset patch
# User mingchen0919
# Date 1506369164 14400
# Node ID e2a0bc241b56bba6560665d9618bce923c72fdd2
# Parent  6afe8433106c859c90a47c3cc5613a2a91a54cb2
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty

diff -r 6afe8433106c -r e2a0bc241b56 collection_list.Rmd
--- a/collection_list.Rmd	Mon Sep 25 15:44:25 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 15:52:44 2017 -0400
@@ -21,11 +21,9 @@
 ```
 
 
-```{bash 'copy data to working directory'}
-mkdir files_directory
-# Copy uploaded data to the working directory
-for f in $(echo FILE_LIST | sed "s/,/ /g")
-do
-    cp $f ./files_directory/$f.fastqsanger
-done
+```{r}
+from_files = strsplit("FILE_LIST", ',')[[1]]
+to_files = gsub('\\.dat', '\\.fastqsanger', from_files)
+file.copy(from_files, to_files)
 ```
+