added procedure switch to find_genes

[biopieces.git] / code_ruby / Maasha / lib / prodigal.rb

diff --git a/code_ruby/Maasha/lib/prodigal.rb b/code_ruby/Maasha/lib/prodigal.rb
index 1a1fd552af5311caf9f8b3ce1bd0187aa6b81007..9ddbf79f62db23cf5d73f3a867933af48f0bd8e3 100644 (file)
--- a/code_ruby/Maasha/lib/prodigal.rb
+++ b/code_ruby/Maasha/lib/prodigal.rb
@@ -42,6 +42,7 @@ class Prodigal
     commands = []
     commands << "prodigal"
     commands << "-c" if @options[:full]
+    commands << "-p #{@options[:procedure]}"
     commands << "-i #{@infile}"
     commands << "-o #{@outfile}"