--- a/phyml_sms.xml	Mon Sep 26 10:32:03 2016 -0400
+++ b/phyml_sms.xml	Mon Sep 26 10:43:57 2016 -0400
@@ -1,15 +1,36 @@
 <tool id="phyml-sms" name="PhyML-SMS" version="1.3.1">
 	<description>Maximum likelihood-based inference of phylogenetic trees with Smart Model Selection</description>
+	<macros>
+        <import>macro_seqtypedetect.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="1.3">phyml-sms</requirement>
     </requirements>
 	<command><![CDATA[
+
+
+
+		## Automatic sequence detection
+		## read an info file to choose which option set
+		#set $info = open( str($input_info) ).read()
+
 		sms.sh
 		-i $input
 		-o .
 		-p $output_models
 		-t
-		-d $sequence.seqtype
+
+		#if $sequence.seqtype == "cfg"
+			## Automatic sequence detection
+			## read an info file to choose which option set
+			#set $info = open( str($input_info) ).read()
+
+			#if 'dna' in $info:
+				-d nt
+			#else if 'protein' in $info :
+				-d aa
+		#else
+			-d $sequence.seqtype
 
    		-c $stat_crit
 				
@@ -43,10 +64,13 @@
 			<param name="seqtype" type="select" label="Data type">
 				<option value="nt">Nucleic acids</option>
 				<option value="aa">Amino acids</option>
+			<when value="cfg">
+                <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" />
+            </when>
 			</param>
 			<when value="nt" />
 			<when value="aa" />
-		</conditional>   
+		</conditional>
 		<param name="stat_crit" type="select" label="Statistical criterion to select the model">
 				<option value="aic">AIC</option>
 				<option value="bic">BIC</option>
@@ -96,12 +120,9 @@
 
 .. class:: infomark
 
-
 This script runs SMS to select the substitution model which best fits the input data.
 It may also run PhyML with the selected model.
-
- SMS options ::
-
+SMS options :
 	 -h = Help
 	 -i = **Mandatory** Input alignment file in PHYLIP format
 	 -d = **Mandatory** Data type : 'aa' or 'nt'
@@ -110,14 +131,11 @@
 	 -c = Statistical criterion to select the model : 'AIC' (default) or 'BIC'
 	 -u = Input starting tree (Newick format)
 	 -t = Use this option if you want SMS to infer a tree with PhyML using the SMS selected model
-
- PhyML options ::
-
+ PhyML options :
 	 -s = Type of tree improvement : 'NNI (default)' or 'SPR'
 	 -r = Number of random starting trees : 0 (default)
 	 -b = Branch Support : >0 for bootstraps, -4 for aLRT, 0 (default)
 
-
 **PhyML 20120412**
 
 -----