diff collection_list.Rmd @ 13:ff1cb127967e draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty

--- a/collection_list.Rmd	Mon Sep 25 16:10:27 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:19:14 2017 -0400
@@ -16,22 +16,12 @@
 
 # Command line arguments
 
-```{r}
+```{r 'command line arguments'}
 str(opt)
 ```
 
 
-```{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
-    sed "s/.dat/"
-    cp $f ./files_directory
-done
-```
-
-```{r}
+```{r 'rename files'}
 # create directory
 dir.create('./files_directory')
 # get full paths of original files
@@ -41,9 +31,10 @@
 # get original file names
 original_files = list.files('./files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '\\.fastqsanger', original_files)
+new_files = gsub('\\.dat', '\\.FORMAT', original_files)
 # rename files
 file.copy(paste0('./files_directory/', original_files),
           paste0('./files_directory/', new_files))
 ```
 
+# End