changeset 16:42cccad7e145 draft

planemo upload commit 09b6a41798350090b61aea16966ba64b583ef02b-dirty

--- a/rmarkdown_report_render.R	Sat Jun 09 10:27:19 2018 -0400
+++ b/rmarkdown_report_render.R	Sat Jun 09 10:41:42 2018 -0400
@@ -13,12 +13,10 @@
 library('getopt')
 library('rmarkdown')
 library('htmltools')
-library('plyr')
-library('dplyr')
-library('stringr')
-library('DT')
-library('reshape2')
+library('ggplot2')
 library('plotly')
+library('DESeq2')
+library('pheatmap')
 #------------------------------------------------------------------
 options(stringsAsFactors = FALSE)
 
@@ -96,7 +94,7 @@
       lapply(dirs, function(x) {
         path_end = tail(strsplit(x, '/')[[1]], 1)
         # hide vakata-jstree-3.3.5 folder
-        if ( !(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files'))) {
+        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"}')
@@ -137,14 +135,12 @@
   # 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,