changeset 11:e5d245413f1b draft default tip

update

--- a/es_gene_search.Rmd	Mon Mar 19 22:44:25 2018 -0400
+++ b/es_gene_search.Rmd	Mon Mar 19 23:55:31 2018 -0400
@@ -1,5 +1,5 @@
 ---
-title: 'HTML report title'
+title: 'Tripal Database: gene search'
 output:
     html_document:
       theme: cosmo
@@ -8,24 +8,28 @@
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = TRUE,
+  echo = FALSE,
   error = TRUE
 )
 ```
 
 
-# Code for computational analysis
+# Search information
 
-```{r 'step 1'}
-opt
+```{r, results='asis'}
+cat('\n')
+cat('* **Database URL**:', opt$X_U, '\n')
+cat('* **Organism**:', opt$X_O, '\n')
+cat('* **Keywords**:', opt$X_K, '\n')
 ```
 
-```{r 'ste[ 2'}
+
+```{r}
 download_url = paste0(opt$X_U, '/elasticsearch/gene_download?',
-             'organism=', RCurl::curlEscape(opt$X_O), '&',
-             'search_term=', RCurl::curlEscape(opt$X_K))
-print(download_url)
+             'organism=', URLencode(opt$X_O), '&',
+             'search_term=', URLencode(opt$X_K))
 download.file(download_url, destfile = opt$X_R)
 ```
 
 
+