# HG changeset patch
# User mingchen0919
# Date 1506443642 14400
# Node ID 68da32dbc6e2a9a4c126b111e0922377356dbfba
# Parent  fb05ca4741270e29c1d6b4d333578536747586df
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty

diff -r fb05ca474127 -r 68da32dbc6e2 collection_list_paired.Rmd
--- a/collection_list_paired.Rmd	Tue Sep 26 12:24:21 2017 -0400
+++ b/collection_list_paired.Rmd	Tue Sep 26 12:34:02 2017 -0400
@@ -67,4 +67,3 @@
 file.copy(paste0('./reverse_files_directory/', original_files),
           paste0('./files_directory/', new_files))
 ```
-
diff -r fb05ca474127 -r 68da32dbc6e2 collection_list_paired_render.R
--- a/collection_list_paired_render.R	Tue Sep 26 12:24:21 2017 -0400
+++ b/collection_list_paired_render.R	Tue Sep 26 12:34:02 2017 -0400
@@ -82,4 +82,4 @@
 render('list_paired_collection.Rmd', output_file = opt$list_paired_collection_html)
 
 
-#-------4. manipulate outputs -----------------------------
+#-------4. manipulate outputs -----------------------------
\ No newline at end of file
diff -r fb05ca474127 -r 68da32dbc6e2 collection_paired_render.R
--- a/collection_paired_render.R	Tue Sep 26 12:24:21 2017 -0400
+++ b/collection_paired_render.R	Tue Sep 26 12:34:02 2017 -0400
@@ -70,10 +70,10 @@
     gsub('FORWARD_INPUT', opt$forward_input, x)
   }) %>%
   (function(x) {
-    gsub('REVERSE_INPUT', opt$reverse_forward_input, x)
+    gsub('REVERSE_INPUT', opt$reverse_input, x)
   }) %>%
   (function(x) {
-    gsub('OUTPUT_DIR', opt$reverse_forward_input, x)
+    gsub('OUTPUT_DIR', opt$paired_collection_dir, x)
   }) %>%
   (function(x) {
     fileConn = file('paired_collection.Rmd')