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planemo upload

---
title: 'HTML report title'
output:
    html_document:
      highlight: pygments
---

```{r, echo=FALSE}
# to make the css theme to work, <link></link> tags cannot be added directly 
# as <script></script> tags as below.
# it has to be added using a code chunk with the htmltool functions!!!
css_link = tags$link()
css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
css_link
```

```{r, eval=FALSE, echo=FALSE}
# this code chunk is purely for adding comments
# below is to add jQuery and jstree javascripts
```
<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
<script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>

```{r, eval=FALSE, echo=FALSE}
# this code chunk is purely for adding comments
# javascript code below is to build the file tree interface
# see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
```
<script>
  $(function () {
    // create an instance when the DOM is ready
    $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
     window.open( data.node.a_attr.href, data.node.a_attr.target )
    });
  });
</script>

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(echo = TRUE, error = TRUE)
```





















# Output

```{bash, echo=FALSE}
# copy jstree directory to output directory
cp -r ${X_t}/vakata-jstree-3.3.5 ${X_d}
```

```{r, echo=FALSE}
# get the OUTPUT_DIR folder data: dataset_NUMBER_files
output_dir = tail(strsplit(opt$X_d, '/')[[1]], 1)
# define a recursive function to build html string of the file tree
file_tree = function(dir = '.'){
  files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
  # files also include directorys, need to remove directorys
  files = files[!dir.exists(files)]
  dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
  tags$ul(
    {
      if (length(files) > 0) {
        lapply(files, function(x){
          path_end = tail(strsplit(x, '/')[[1]],1)
          href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
          li_item = tags$li(tags$a(path_end, href=href_path))
          li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
          li_item
        })
      }
    },
    {
      if (length(dirs) > 0) {
        lapply(dirs, function(x){
          x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
          li_item = tags$li(x_path, file_tree(x))
          li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
          li_item
        })
      }
    }
  )
}
```

```{r, echo=FALSE}
# create a div container to store the file tree interface
tags$div(
  id="jstree",
  file_tree(opt$X_d)
)
```