# HG changeset patch
# User mingchen0919
# Date 1506395924 14400
# Node ID 025ca0833787bc2f24cfccf3c894615d87c1789b
# Parent  a25b427a1f389f264cc5e254a93609806e63d581
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty

diff -r a25b427a1f38 -r 025ca0833787 collection_list_paired_render.R
--- a/collection_list_paired_render.R	Mon Sep 25 23:15:32 2017 -0400
+++ b/collection_list_paired_render.R	Mon Sep 25 23:18:44 2017 -0400
@@ -36,7 +36,7 @@
 spec_list$FORMAT = c('format', 'f', '1', 'character')
 ##--------2. output report and outputs --------------
 spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character')
-spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character')
+spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character')
 ##--------3. Rmd templates in the tool directory ----------
 spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character')
 
@@ -50,7 +50,7 @@
 library(dplyr)
 
 #----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$list_collection_dir))
+system(paste0('mkdir -p ', opt$list_paired_collection_dir))
 
 #----- 2. generate Rmd files with Rmd templates --------------
 #   a. templates without placeholder variables:
@@ -73,9 +73,6 @@
     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)