fix one bug relating to outputs and enhance documentation

Author: bgruening

Diff for: EDeN/EDeN_test.xml

@@ -13,13 +13,13 @@
 
         --model_file_name $model_infile
 
-        --minimal_output 
+        --minimal_output
 
     </command>
     <inputs>
-        <param format="eden_sparse_vector" name="sparse_vector_infile" type="data" label="Input File" help=""/>
-        <param format="txt" name="model_infile" type="data" label="Input Model" 
-            help="created with the EDeN Train program"/>
+        <param format="eden_sparse_vector" name="sparse_vector_infile" type="data" label="Input File" help="Sparse Vector file, created with EDeN convert." />
+        <param format="txt" name="model_infile" type="data" label="Input Model"
+            help="Created with EDeN Train."/>
 
         <expand macro="kernel_type_options" />
 
@@ -29,7 +29,8 @@
 
     </inputs>
     <outputs>
-        <data format="tabular" name="output" from_work_dir="prediction" label="Generated from ${on_string}"/>
+        <data format="tabular" name="prediction" from_work_dir="prediction" label="EDeN on ${on_string}: Prediction"/>
+        <data format="tabular" name="margin" from_work_dir="margin" label="EDeN on ${on_string}: Margin"/>
     </outputs>
     <tests>
         <test>

Diff for: EDeN/EDeN_train.xml

@@ -33,10 +33,9 @@
             --only_negative $supervised_opts.only_negative
         #end if
 
-
     </command>
     <inputs>
-        <param format="eden_sparse_vector" name="infile" type="data" label="Input Graph" help=""/>
+        <param format="eden_sparse_vector" name="infile" type="data" label="Input File" help="Sparse Vector file, created with EDeN convert."/>
         <param format="txt" name="target_infile" type="data" label="Target file" help="indicates with -1 and 1 the class"/>
 
         <param name="epoch" type="integer" value="10" label="Epoch, Stochastic gradient descend algorithm." help="">
@@ -62,7 +61,7 @@
             </param>
             <when value="non">
             </when>
-            <when value="">
+            <when value="supervised">
                 <!-- 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.">