# HG changeset patch
# User mingchen0919
# Date 1506396960 14400
# Node ID 8800e1a70b20771f1884ca3b8c8c3e5a4da14796
# Parent  882d249a641802d277ee7ad5f8e69d4e240a4e2c
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty

diff -r 882d249a6418 -r 8800e1a70b20 collection_list_paired.Rmd
--- a/collection_list_paired.Rmd	Mon Sep 25 23:30:06 2017 -0400
+++ b/collection_list_paired.Rmd	Mon Sep 25 23:36:00 2017 -0400
@@ -61,6 +61,6 @@
 new_files = gsub('\\.dat', '_2\\.FORMAT', original_files)
 # rename files
 file.copy(paste0('./reverse_files_directory/', original_files),
-          paste0('./files_directory/', new_files))
+          paste0('./', new_files))
 ```
 
diff -r 882d249a6418 -r 8800e1a70b20 collection_list_paired.xml
--- a/collection_list_paired.xml	Mon Sep 25 23:30:06 2017 -0400
+++ b/collection_list_paired.xml	Mon Sep 25 23:36:00 2017 -0400
@@ -47,7 +47,7 @@
     <outputs>
         <data format="html" name="report" label="Collection builder (list:paired collection)" />
         <collection type="list:paired" name="list_collection">
-            <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
+            <discover_datasets pattern="__name_and_ext__" visible="true" />
         </collection>
     </outputs>
 </tool>
\ No newline at end of file
diff -r 882d249a6418 -r 8800e1a70b20 collection_list_paired_render.R
--- a/collection_list_paired_render.R	Mon Sep 25 23:30:06 2017 -0400
+++ b/collection_list_paired_render.R	Mon Sep 25 23:36:00 2017 -0400
@@ -73,6 +73,9 @@
     gsub('REVERSE_FILE_LIST', opt$reverse_file_list, x)
   }) %>%
   (function(x) {
+    gsub('OUTPUT_DIR', opt$list_paired_collection_dir, x)
+  }) %>%
+  (function(x) {
     fileConn = file('list_paired_collection.Rmd')
     writeLines(x, con=fileConn)
     close(fileConn)