# HG changeset patch
# User mingchen0919
# Date 1506457338 14400
# Node ID f555686ca340427b244e2a5eccc417f548aa716b
# Parent  abf9cbd7578f1c39da95cd915dc01ef071ce6b54
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db-dirty

diff -r abf9cbd7578f -r f555686ca340 collection_list_paired.Rmd
--- a/collection_list_paired.Rmd	Tue Sep 26 13:43:32 2017 -0400
+++ b/collection_list_paired.Rmd	Tue Sep 26 16:22:18 2017 -0400
@@ -40,9 +40,7 @@
 # get original file names
 original_files = list.files('./forward_files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '_forward\\.FORMAT', original_files)
 new_files = paste0('input', 1:length(original_files), '_forward.FORMAT')
-new_files
 # rename files
 file.copy(paste0('./forward_files_directory/', original_files),
           paste0('./files_directory/', new_files))
@@ -60,9 +58,7 @@
 # get original file names
 original_files = list.files('./reverse_files_directory')
 # create new files names from original file names
-new_files = gsub('\\.dat', '_reverse\\.FORMAT', original_files)
 new_files = paste0('input', 1:length(original_files), '_reverse.FORMAT')
-new_files
 # rename files
 file.copy(paste0('./reverse_files_directory/', original_files),
           paste0('./files_directory/', new_files))
diff -r abf9cbd7578f -r f555686ca340 collection_paired.Rmd
--- a/collection_paired.Rmd	Tue Sep 26 13:43:32 2017 -0400
+++ b/collection_paired.Rmd	Tue Sep 26 16:22:18 2017 -0400
@@ -23,7 +23,8 @@
 # Rename files
 
 ```{r}
-file.copy("FORWARD_INPUT", './forward.FORMAT')
-file.copy("REVERSE_INPUT", './reverse.FORMAT')
+dir.create('files_directory')
+file.copy("FORWARD_INPUT", './files_directory/forward.FORMAT')
+file.copy("REVERSE_INPUT", './files_directory/reverse.FORMAT')
 ```
 
diff -r abf9cbd7578f -r f555686ca340 collection_paired.xml
--- a/collection_paired.xml	Tue Sep 26 13:43:32 2017 -0400
+++ b/collection_paired.xml	Tue Sep 26 16:22:18 2017 -0400
@@ -47,6 +47,7 @@
     <outputs>
         <data format="html" name="report" label="Collection builder (paired collection)" />
         <collection type="paired" name="list_collection">
+            <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
         </collection>
     </outputs>
 </tool>
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