# HG changeset patch
# User mingchen0919
# Date 1506371634 14400
# Node ID cb6efa0f0cb66ca6953e7aee003bbe8e55c88f4f
# Parent  56b68a320c0e83a7d641716b6e0917d8b3737b7c
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 93b036c66fd754a7af459fa80d3f7f143a68477b-dirty

diff -r 56b68a320c0e -r cb6efa0f0cb6 collection_list.Rmd
--- a/collection_list.Rmd	Mon Sep 25 16:25:35 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:33:54 2017 -0400
@@ -38,3 +38,8 @@
 ```
 
 # End
+
+```{r 'test'}
+ls()
+```
+
diff -r 56b68a320c0e -r cb6efa0f0cb6 collection_list_render.R
--- a/collection_list_render.R	Mon Sep 25 16:25:35 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 16:33:54 2017 -0400
@@ -34,7 +34,7 @@
 spec_list$ECHO = c('echo', 'e', '1', 'character')
 spec_list$FORMAT = c('format', 'f', '1', 'character')
 ##--------2. output report and outputs --------------
-spec_list$REPORT = c('report', 'r', '1', 'character')
+spec_list$OUTPUT_HTML = c('list_collection_html', 'r', '1', 'character')
 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
@@ -78,6 +78,7 @@
   })
 
 #------ 3. render all Rmd files --------
-render('list_collection.Rmd', output_file = opt$report)
+render('list_collection.Rmd', output_file = opt$list_collection_html)
+cat('test')
 
 #-------4. manipulate outputs -----------------------------