# HG changeset patch
# User mingchen0919
# Date 1528554439 14400
# Node ID b3ea48ff4fe3416ce65c9c29b09442f5a0cb050e
# Parent  16b2b7c3606e86534abc3e0703e1cf81fc5158a1
planemo upload commit 9d7c251123a0111cb00bb7c38e58231ea707d21d-dirty

diff -r 16b2b7c3606e -r b3ea48ff4fe3 rmarkdown_report_render.R
--- a/rmarkdown_report_render.R	Mon May 14 14:30:55 2018 -0400
+++ b/rmarkdown_report_render.R	Sat Jun 09 10:27:19 2018 -0400
@@ -13,10 +13,12 @@
 library('getopt')
 library('rmarkdown')
 library('htmltools')
-library('ggplot2')
+library('plyr')
+library('dplyr')
+library('stringr')
+library('DT')
+library('reshape2')
 library('plotly')
-library('DESeq2')
-library('pheatmap')
 #------------------------------------------------------------------
 options(stringsAsFactors = FALSE)
 
@@ -94,7 +96,7 @@
       lapply(dirs, function(x) {
         path_end = tail(strsplit(x, '/')[[1]], 1)
         # hide vakata-jstree-3.3.5 folder
-        if (path_end != 'vakata-jstree-3.3.5') {
+        if ( !(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files'))) {
           # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
           li_item = tags$li(path_end, file_tree(x))
           li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
@@ -135,12 +137,14 @@
   # render a single html
   system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
   # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
-  jstree_lines = '
+  jstree_lines = 
+'
 ## Outputs
 
 ```{r, echo=FALSE}
 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
-```'
+```
+'
   write(
     x = jstree_lines,
     append = TRUE,