# HG changeset patch
# User mingchen0919
# Date 1521513054 14400
# Node ID dbe86b15ee8b29c369dc724f2af9f1b20cbe673a
# Parent faddfcea253d07e9bf1f2d5839d338997bc76e33
add r-rcurl
diff -r faddfcea253d -r dbe86b15ee8b es_gene_search.Rmd
--- a/es_gene_search.Rmd Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.Rmd Mon Mar 19 22:30:54 2018 -0400
@@ -21,7 +21,11 @@
```
```{r 'ste[ 2'}
-
+download_url = paste0(opt$X_U, '/elasticsearch/gene_download?',
+ 'organism=', RCurl::curlEscape(opt$X_O), '&',
+ 'search_term=', RCurl::curlEscape(opt$X_K))
+print(download_url)
+download.file(download_url, destfile = opt$X_R)
```
diff -r faddfcea253d -r dbe86b15ee8b es_gene_search.csv
--- a/es_gene_search.csv Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.csv Mon Mar 19 22:30:54 2018 -0400
@@ -1,5 +1,7 @@
short flag,argument mask,data type,variable name,galaxy input type,description
o,1,character,report,data,
d,1,character,report.files_path,data,
+U,1,character,tripal_db_url,text,
O,1,character,organism,text,
+K,1,character,search_keywords,text,
R,1,character,fasta_results,text,
diff -r faddfcea253d -r dbe86b15ee8b es_gene_search.sh
--- a/es_gene_search.sh Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.sh Mon Mar 19 22:30:54 2018 -0400
@@ -4,5 +4,7 @@
-o '$report'
-d '$report.files_path'
+ -U '$tripal_db_url'
-O '$organism'
+ -K '$search_keywords'
-R '$fasta_results'
diff -r faddfcea253d -r dbe86b15ee8b es_gene_search.xml
--- a/es_gene_search.xml Mon Mar 19 17:41:50 2018 -0400
+++ b/es_gene_search.xml Mon Mar 19 22:30:54 2018 -0400
@@ -1,37 +1,25 @@
-
-
- pandoc
- r-getopt
- r-rmarkdown
- r-jsonlite
- r-dt
- r-curl
-
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+
+ pandocr-getoptr-rmarkdownr-jsonliter-dtr-curlr-rcurl
+
+
+
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+ ]]>
diff -r faddfcea253d -r dbe86b15ee8b get_content_types.xml
--- a/get_content_types.xml Mon Mar 19 17:41:50 2018 -0400
+++ b/get_content_types.xml Mon Mar 19 22:30:54 2018 -0400
@@ -1,18 +1,10 @@
-
-
- pandoc
- r-getopt
- r-rmarkdown
- r-jsonlite
- r-dt
- r-curl
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+
+ pandocr-getoptr-rmarkdownr-jsonliter-dtr-curlr-rcurl
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+ ]]>
diff -r faddfcea253d -r dbe86b15ee8b search_contents.xml
--- a/search_contents.xml Mon Mar 19 17:41:50 2018 -0400
+++ b/search_contents.xml Mon Mar 19 22:30:54 2018 -0400
@@ -1,19 +1,11 @@
-
+
-
- pandoc
- r-getopt
- r-rmarkdown
- r-jsonlite
- r-dt
- r-curl
-
-
-
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-
+ pandocr-getoptr-rmarkdownr-jsonliter-dtr-curlr-rcurl
+
+
+
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+ ]]>