Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

diff collection_list_render.R @ 8:9c2059916485 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 15:30:55 -0400
parents 2730c4979dcb
children ff1cb127967e
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--- a/collection_list_render.R	Mon Sep 25 15:19:06 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 15:30:55 2017 -0400
@@ -33,7 +33,6 @@
 spec_list$FILE_LIST = c('file_list', 'l', '1', 'character')
 spec_list$ECHO = c('echo', 'e', '1', 'character')
 ##--------2. output report and outputs --------------
-# spec_list$LIST_COLLECTION = c('list_collection', 'o', '1', 'character')
 spec_list$REPORT = c('report', 'r', '1', 'character')
 spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
@@ -75,6 +74,6 @@
   })
 
 #------ 3. render all Rmd files --------
-render('list_collection.Rmd', output_file = opt$list_collection_html)
+render('list_collection.Rmd', output_file = opt$report)
 
 #-------4. manipulate outputs -----------------------------