--- a/collection_list.Rmd	Mon Sep 25 14:28:52 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:19:52 2017 -0400
@@ -14,16 +14,27 @@
 )
 ```
 
-```{r}
+# Command line arguments
+
+```{r 'command line arguments'}
 str(opt)
 ```
 
 
-```{bash 'copy data to working directory', echo=FALSE}
-mkdir files_directory
-# Copy uploaded data to the working directory
-for f in $(echo FILE_LIST | sed "s/,/ /g")
-do
-    cp $f ./files_directory
-done
-```
\ No newline at end of file
+```{r 'rename files'}
+# create directory
+dir.create('./files_directory')
+# get full paths of original files
+from_files = strsplit("FILE_LIST", ',')[[1]]
+# copy files to the created directory.
+file.copy(from_files, './files_directory')
+# get original file names
+original_files = list.files('./files_directory')
+# create new files names from original file names
+new_files = gsub('\\.dat', '\\.FORMAT', original_files)
+# rename files
+file.copy(paste0('./files_directory/', original_files),
+          paste0('./files_directory/', new_files))
+```
+
+# End