changeset 8:9c2059916485 draft

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 566d487c9518
children 9cf2069b31c0
files collection_list.Rmd collection_list_render.R
diffstat 2 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/collection_list.Rmd	Mon Sep 25 15:19:06 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 15:30:55 2017 -0400
@@ -14,12 +14,14 @@
 )
 ```
 
+# Command line arguments
+
 ```{r}
 str(opt)
 ```
 
 
-```{bash 'copy data to working directory', echo=FALSE}
+```{bash 'copy data to working directory'}
 mkdir files_directory
 # Copy uploaded data to the working directory
 for f in $(echo FILE_LIST | sed "s/,/ /g")
--- a/collection_list_render.R	Mon Sep 25 15:19:06 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 15:30:55 2017 -0400
@@ -33,7 +33,6 @@
 spec_list$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 -----------------------------