# HG changeset patch
# User mingchen0919
# Date 1504057708 14400
# Node ID d41a3115e470ab47e680c2794f7705d7d2b99b9a
# Parent  fcd72af3f41e4adec4ae1b67458040d2fee65da3
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 377565cfe72b3455320ea04b7c58191bf4428d79-dirty

diff -r fcd72af3f41e -r d41a3115e470 i_adhore_configure.Rmd
--- a/i_adhore_configure.Rmd	Tue Aug 29 17:57:47 2017 -0400
+++ b/i_adhore_configure.Rmd	Tue Aug 29 21:48:28 2017 -0400
@@ -12,20 +12,10 @@
 knitr::opts_chunk$set(echo = ECHO)
 ```
 
+```{r echo=FALSE}
 # Genomes and analysis files
-
-```{r}
 g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]]
 g_analysis_files_list = list()
-# for(i in g_analysis_files_set) {
-#   genome = strsplit(i, ':')[[1]][1]
-#   analysis_files = strsplit(i, ':')[[1]][2] %>% 
-#                       strsplit(',') %>% `[[`(1) %>% 
-#                       (function(x){
-#                         paste0(1:length(x),' ', x)
-#                       })
-#   g_analysis_files_list[[genome]] = analysis_files
-# }
 for(i in g_analysis_files_set) {
   genome = strsplit(i, ':')[[1]][1]
   analysis_files = strsplit(i, ':')[[1]][2] %>% 
@@ -39,12 +29,12 @@
     'name' = paste0('genome=', strsplit(i, ':')[[1]][1]),
     'analysis_files' = analysis_files
   )
-  print(paste0('genome=', strsplit(i, ':')[[1]][1]))
-  print(analysis_files)
+  #print(paste0('genome=', strsplit(i, ':')[[1]][1]))
+  #print(analysis_files)
 }
 ```
 
-# Other parameters
+# Tool parameters
 
 ```{r}
 output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1)
@@ -85,7 +75,7 @@
 
 ```{bash}
 # run i-adhore analysis
-i-adhore I_ADHORE_CONFIGURE_TXT
+i-adhore I_ADHORE_CONFIGURE_TXT > /dev/null 2>&1
 ```
 
 Links to outputs