diff rmarkdown_report.Rmd @ 1:e0828838e0f3 draft default tip

update

--- a/rmarkdown_report.Rmd	Fri Nov 09 13:29:21 2018 -0500
+++ b/rmarkdown_report.Rmd	Fri Nov 09 15:25:01 2018 -0500
@@ -1,5 +1,5 @@
 ---
-title: 'Aurora Tool Report'
+title: 'Dustmasker Report'
 output:
     html_document:
       highlight: pygments
@@ -54,23 +54,21 @@
 ---
 
 
-## Run `dustmasker`
+## Run `dustmasker` job
 
-```{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
+```{bash echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/scripts_generator.sh
 ```
 
-Options explanation:
+```{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>
@@ -98,5 +96,4 @@
    
  -out <File_Out>
    output file name
-   Default = `-'
 </pre>
\ No newline at end of file