# HG changeset patch
# User mingchen0919
# Date 1502825723 14400
# Node ID dab02b629d48ebd5af5b75d1bd7e83906a93f442
# Parent  85166d75910bf94caef23e6e99b9560f198f052b
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 60ea96204588be4348bd5d7879d1eb0d73f487c7-dirty

diff -r 85166d75910b -r dab02b629d48 i_adhore_configure.Rmd
--- a/i_adhore_configure.Rmd	Tue Aug 08 16:45:49 2017 -0400
+++ b/i_adhore_configure.Rmd	Tue Aug 15 15:35:23 2017 -0400
@@ -47,17 +47,21 @@
 # Other parameters
 
 ```{r}
+data_dir = gsub('dataset_.*dat', '', opt$blast_table)
+output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1)
+output_path = paste(data_dir, output_dir, sep = '')
+                  
 params = c(
-  'blast table' = opt$blast_table,
-  'output_path' = opt$i_adhore_configure_dir,
+  'blast_table' = opt$blast_table,
+  'output_path' = output_path,
   'gap_size' = opt$gap_size,
   'cluster_gap' = opt$cluster_gap,
   'q_value' = opt$q_value,
   'prob_cutoff' = opt$prob_cutoff,
   'anchor_points' = opt$anchor_points,
-  'level_2_only' = opt$level2only,
+  'level_2_only' = tolower(opt$level2only),
   'table_type' = opt$table_type,
-  'multi_hypothesis_correction' = opt$multi_hypothesis_correction
+  'multiple_hypothesis_correction' = opt$multi_hypothesis_correction
 )
 
 df = data.frame(name = names(params),
@@ -71,7 +75,7 @@
 lines = c(unlist(g_analysis_files_list), 
           ' ', 
           paste0(df$name, '=', df$value), 
-          'CompareAligners')
+          'compareAligners')
 fileConn = file('I_ADHORE_CONFIGURE_TXT')
 writeLines(lines, con = fileConn)
 ```