view rmarkdown_report.Rmd @ 0:389ef73cf4e1 draft

planemo upload

---
title: 'Aurora Tool Report'
output:
    html_document:
      highlight: pygments
---

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

```{css echo=FALSE}
# code chunks scrollable
pre code, pre, code {
  white-space: pre !important;
  overflow-x: scroll !important;
  word-break: keep-all !important;
  word-wrap: initial !important;
}
```


```{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>

---
# 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>

---
# ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
---

# Run `findSRRs_altered.pl`

* `${REPORT_FILES_PATH}`: the output directory that stores all analysis outputs.
* `${TOOL_INSTALL_DIR}`: the tool install directory where the `findSSRs_altered.pl` is located.
* `$X_f`: the path to the fasta file.
* `$X_m`: the path to the masked fasta file.

```{bash}
cd ${REPORT_FILES_PATH}
perl ${TOOL_INSTALL_DIR}/findSSRs_altered.pl \
  -f $X_f \
  -m $X_m
```