diff collection_list_paired.Rmd @ 20:975365a3e126 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty

--- a/collection_list_paired.Rmd	Mon Sep 25 22:59:34 2017 -0400
+++ b/collection_list_paired.Rmd	Mon Sep 25 23:07:31 2017 -0400
@@ -25,37 +25,42 @@
 ## Forward inputs
 
 ```{r 'create inputs directory'}
-# create directory
+# create directory to store both forward and reverse inputs
+# this is the directory where datasets will be discovered.
 dir.create('./files_directory')
 ```
 
 ```{r 'rename forward files'}
+# create directory
+dir.create('./forward_files_directory')
 # get full paths of original files
 from_files = strsplit("FORWARD_FILE_LIST", ',')[[1]]
-# copy files to the created directory.
-file.copy(from_files, './files_directory')
+# copy files to forward_files_directory.
+file.copy(from_files, './forward_files_directory')
 # get original file names
-original_files = list.files('./files_directory')
+original_files = list.files('./forward_files_directory')
 # create new files names from original file names
 new_files = gsub('\\.dat', '_1\\.FORMAT', original_files)
 # rename files
-file.copy(paste0('./files_directory/', original_files),
+file.copy(paste0('./forward_files_directory/', original_files),
           paste0('./files_directory/', new_files))
 ```
 
 ## Reverse inputs
 
 ```{r 'rename reverse files'}
+# create directory
+dir.create('./reverse_files_directory')
 # get full paths of original files
-from_files = strsplit("REVERSE_FILE_LIST", ',')[[1]]
-# copy files to the created directory.
-file.copy(from_files, './files_directory')
+from_files = strsplit("reverse_FILE_LIST", ',')[[1]]
+# copy files to reverse_files_directory.
+file.copy(from_files, './reverse_files_directory')
 # get original file names
-original_files = list.files('./files_directory')
+original_files = list.files('./reverse_files_directory')
 # create new files names from original file names
 new_files = gsub('\\.dat', '_2\\.FORMAT', original_files)
 # rename files
-file.copy(paste0('./files_directory/', original_files),
+file.copy(paste0('./reverse_files_directory/', original_files),
           paste0('./files_directory/', new_files))
 ```