From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 10 May 2011 10:30:30 +0000 (+0000)
Subject: added procedure switch to analyze_assembly
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a62ae8fdb575f309a8d60d143b9d367f620abf1e;p=biopieces.git

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 89b7b32..b30517a 100755
--- 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