Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

changeset 11:e2a0bc241b56 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 15:52:44 -0400
parents 6afe8433106c
children f5b1f7d4db53
files collection_list.Rmd
diffstat 1 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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)
 ```
+