# HG changeset patch
# User mingchen0919
# Date 1522674977 14400
# Node ID 4f9f1e76f7e6ed7cf02f049264d035edcf744ac1
# Parent  9ff33a3631fa7bc59b653eeab22912eb05f53215
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty

diff -r 9ff33a3631fa -r 4f9f1e76f7e6 individuals.Rmd
--- a/individuals.Rmd	Mon Apr 02 08:32:59 2018 -0400
+++ b/individuals.Rmd	Mon Apr 02 09:16:17 2018 -0400
@@ -44,7 +44,6 @@
     if (file.exists(full_path)) {
       # to_files = list.files(full_path)
       to_file = tail(strsplit(full_path, '/')[[1]], 1)
-      print(to_file)
       file.copy(from = full_path, to = paste0(individual_outputs_path, to_file))
     }
     # command_line = paste0('cp -r ', full_path, ' paired')
diff -r 9ff33a3631fa -r 4f9f1e76f7e6 list.Rmd
--- a/list.Rmd	Mon Apr 02 08:32:59 2018 -0400
+++ b/list.Rmd	Mon Apr 02 09:16:17 2018 -0400
@@ -30,14 +30,25 @@
 ```
 
 ```{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'])
-    command_line = paste0('cp -r ', full_path, ' list')
-    write(command_line, append = TRUE, 
-          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+    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)
+    }
+    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'))
   }
 }
 ```
diff -r 9ff33a3631fa -r 4f9f1e76f7e6 list_paired.Rmd
--- a/list_paired.Rmd	Mon Apr 02 08:32:59 2018 -0400
+++ b/list_paired.Rmd	Mon Apr 02 09:16:17 2018 -0400
@@ -30,14 +30,25 @@
 ```
 
 ```{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'])
-    command_line = paste0('cp -r ', full_path, ' list_paired')
-    write(command_line, append = TRUE, 
-          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+    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)
+    }
+    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'))
   }
 }
 ```
diff -r 9ff33a3631fa -r 4f9f1e76f7e6 list_paired_render.R
--- a/list_paired_render.R	Mon Apr 02 08:32:59 2018 -0400
+++ b/list_paired_render.R	Mon Apr 02 09:16:17 2018 -0400
@@ -20,6 +20,9 @@
 # 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'),
@@ -30,7 +33,7 @@
 # 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)
diff -r 9ff33a3631fa -r 4f9f1e76f7e6 list_render.R
--- a/list_render.R	Mon Apr 02 08:32:59 2018 -0400
+++ b/list_render.R	Mon Apr 02 09:16:17 2018 -0400
@@ -19,6 +19,9 @@
 # create three folders within working directory
 dir.create('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.
 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list.Rmd'),
@@ -29,7 +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')
 #------------------------------------------