# HG changeset patch
# User mingchen0919
# Date 1522680785 14400
# Node ID 23cbb0daf18d8e8fed045acb25cf5eacd96cd22c
# Parent  52ecc1cfd205a22e0627a441cbe49313924e21b5
planemo upload commit d1d9c6fc42729b4194adac13d1b71062bf19ad0b-dirty

diff -r 52ecc1cfd205 -r 23cbb0daf18d list.Rmd
--- a/list.Rmd	Mon Apr 02 10:21:30 2018 -0400
+++ b/list.Rmd	Mon Apr 02 10:53:05 2018 -0400
@@ -30,25 +30,18 @@
 ```
 
 ```{r, echo=FALSE}
-# write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
 if (nrow(df) > 0) {
   for (i in 1:nrow(df)) {
     tool_output_dir = readLines(df[i, 'tool_output_dir'])[1]
     full_path = paste0(tool_output_dir, '/', df[i, 'relative_path'])
+    # if it is a directory path, add '/*' to the end.
     if (dir.exists(full_path)) {
-      from_files = list.files(full_path, full.names = TRUE)
-      to_files = list.files(full_path)
-      to_files = paste0(list_path, to_files)
-      file.copy(from = from_files, to = to_files)
+      full_path = paste0(full_path, '/*')
     }
-    if (file.exists(full_path)) {
-      # to_files = list.files(full_path)
-      to_file = tail(strsplit(full_path, '/')[[1]], 1)
-      file.copy(from = full_path, to = paste0(list_path, to_file))
-    }
-    # command_line = paste0('cp -r ', full_path, ' paired')
-    # write(command_line, append = TRUE, 
-    #       file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+    command_line = paste0('cp -r ', full_path, ' list')
+    write(command_line, append = TRUE, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
   }
 }
 ```
diff -r 52ecc1cfd205 -r 23cbb0daf18d list_render.R
--- a/list_render.R	Mon Apr 02 10:21:30 2018 -0400
+++ b/list_render.R	Mon Apr 02 10:53:05 2018 -0400
@@ -19,8 +19,8 @@
 # create three folders within working directory
 dir.create('list')
 
-job_working_dir = getwd()
-list_path = paste0(job_working_dir, '/list/')
+# job_working_dir = getwd()
+# list_path = paste0(job_working_dir, '/list/')
 
 #-----------------render Rmd--------------
 # copy R markdown file to working directory and render it within the working directory.
@@ -32,7 +32,7 @@
 # the solution is to render the rmarkdown to a explicitly specified file and then copy the
 # file to ${REPORT}
 system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
-# system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
+system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
 #------------------------------------------