comparison rmarkdown_report.Rmd @ 1:e0828838e0f3 draft default tip

update

0:b8c76b06d724

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

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


## Run `dustmasker`

```{bash}
dustmasker \
  -in $X_A \
  -window $X_B \
  -level $X_C \
  -linker $X_D \
  -infmt $X_E \
  -outfmt $X_F \
  
  $(if [ "$X_G" = "NO_ARGUMENT_YES"  ]; then echo '-parse_seqids'; fi) \
  
  -out dustmasker_out
```

Options explanation:

<pre>
-in <File_In>
   input file name
   Default = `-'

 -parse_seqids
   Parse Seq-ids in FASTA input
   
 -out <File_Out>
   output file name
   Default = `-'
</pre>

1:e0828838e0f3

---
title: 'Dustmasker Report'
output:
    html_document:
      highlight: pygments
---

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


## Run `dustmasker` job

```{bash echo=FALSE}
sh ${TOOL_INSTALL_DIR}/scripts_generator.sh
```

```{r echo=FALSE,warning=FALSE,results='asis'}
# display content of the job-script.sh file.
cat('```bash\n')
cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/dustmasker.sh')), sep = '\n')
cat('\n```')
```


**Options explanation:**

<pre>
-in <File_In>
   input file name
   Default = `-'

 -parse_seqids
   Parse Seq-ids in FASTA input
   
 -out <File_Out>
   output file name
</pre>