--- a/EDeN_train.xml	Tue Oct 29 11:07:49 2013 -0400
+++ b/EDeN_train.xml	Mon Jan 13 09:28:44 2014 -0500
@@ -27,12 +27,16 @@
         --topological_regularization_num_neighbors $topological_regularization_num_neighbors
         --topological_regularization_decay_rate $topological_regularization_decay_rate
 
-        --num_iterations $num_iterations
-        --threshold $threshold
-        --only_positive $only_positive
-        --only_negative $only_negative
+        --random_seed $random_seed
 
-        --random_seed $random_seed
+        ## only if it is semisupervised
+        #if $supervised_opts.supervised_opts_selector != 'non':
+            --num_iterations $supervised_opts.num_iterations
+            --threshold $supervised_opts.threshold
+            --only_positive $supervised_opts.only_positive
+            --only_negative $supervised_opts.only_negative
+        #end if
+
 
     </command>
     <inputs>
@@ -43,16 +47,7 @@
             <validator type="in_range" min="1" />
         </param>
         <param name="lambda" type="text" value="1e-4" label="lambda, Stochastic gradient descend algorithm." help="" />
-
-        <!-- Semi-supervised-settings -->
-        <param name="threshold" type="float" value="1.0" label="Top and low quantile" 
-            help="Only the top and low quantile will be used as positives and negative instances. A threshold of 1 means that all unsupervised instaces are used in the next phase.">
-            <validator type="in_range" min="0.0" />
-        </param>
-        <param name="num_iterations" type="integer" value="3" label="Number of iterations" />
-        <param name="only_negative" type="boolean" label="Induce only negative class instances." truevalue="--only_negative" falsevalue="" checked="false" />
-        <param name="only_positive" type="boolean" label="Induce only positive class instances." truevalue="--only_positive" falsevalue="" checked="false" />
-
+        <param name="random_seed" type="integer" value="1" label="Random Seed" help="" />
 
         <param name="topological_regularization_decay_rate" type="float" value="0.01" label="Topological regularization decay rate">
             <validator type="in_range" min="0.0" />
@@ -64,8 +59,24 @@
             <validator type="in_range" min="0" />
         </param>
 
-        <param name="random_seed" type="integer" value="1" label="Random Seed" help="" />
-
+        <conditional name="supervised_opts">
+            <param name="supervised_opts_selector" type="select" label="Type of the Kernel">
+                <option value="non">non supervised leraning</option>
+                <option value="supervised">supervised learning</option>
+            </param>
+            <when value="non">
+            </when>
+            <when value="">
+                <!-- Semi-supervised-settings -->
+                <param name="threshold" type="float" value="1.0" label="Top and low quantile" 
+                    help="Only the top and low quantile will be used as positives and negative instances. A threshold of 1 means that all unsupervised instaces are used in the next phase.">
+                    <validator type="in_range" min="0.0" />
+                </param>
+                <param name="num_iterations" type="integer" value="3" label="Number of iterations" />
+                <param name="only_negative" type="boolean" label="Induce only negative class instances." truevalue="--only_negative" falsevalue="" checked="false" />
+                <param name="only_positive" type="boolean" label="Induce only positive class instances." truevalue="--only_positive" falsevalue="" checked="false" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="txt" name="model_outfile" label="Train Model from ${on_string}"/>