changeset 6:52ecc1cfd205 draft

planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty

--- a/list_paired.Rmd	Mon Apr 02 09:16:17 2018 -0400
+++ b/list_paired.Rmd	Mon Apr 02 10:21:30 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_paired_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_paired_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_paired')
+    write(command_line, append = TRUE, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
   }
 }
 ```

--- a/list_paired_render.R	Mon Apr 02 09:16:17 2018 -0400
+++ b/list_paired_render.R	Mon Apr 02 10:21:30 2018 -0400
@@ -20,9 +20,6 @@
 # create three folders within working directory
 dir.create('list_paired')
 
-job_working_dir = getwd()
-list_paired_path = paste0(job_working_dir, '/list_paired/')
-
 #-----------------render Rmd--------------
 # copy R markdown file to working directory and render it within the working directory.
 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list_paired.Rmd'),
@@ -33,7 +30,7 @@
 # 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')
 
 # rename files so that all files have the name pattern BASENAME_forward.EXT and BASENAME_reverse.EXT
 from_files = list.files('list_paired', full.names = TRUE)