added procedure switch to analyze_assembly

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1393 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
index 89b7b32ce6f64e778d395b511a9271db6be66f07..b30517ac0fc322fbe9f97e3101ee108f048a4f22 100755 (executable)
--- a/bp_bin/analyze_assembly
+++ b/bp_bin/analyze_assembly
@@ -35,9 +35,10 @@ require 'prodigal'
 require 'pp'
 
 casts = []
-casts << {:long=>'gene_cov',  :short=>'g', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'data_out',  :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'gene_cov',  :short=>'g', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'full',      :short=>'p', :type=>'procedure', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'data_out',  :short=>'o', :type=>'file',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
 
 bp = Biopieces.new