--- a/feature_linker_unlabeled.xml	Fri May 10 17:31:59 2013 -0400
+++ b/feature_linker_unlabeled.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Labeled)">
+<tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Unlabeled)">
   <description>
     Groups corresponding features from multiple maps.
   </description>
@@ -12,23 +12,31 @@
   </command>
   <configfiles>
     <configfile name="config">[simple_options]
-in=$input1
+in=${",".join(map(str, $inputs))}
 out=$output
+#if $type.input_type == "consensusxml"
+$keep_subelements
+#end if
+$ignore_charge
+$use_identifications
+algorithm!second_nearest_gap=$second_nearest_gap
+algorithm!distance_RT!max_difference=$rt_max_difference
+algorithm!distance_MZ!max_difference=$mz_max_difference
+algorithm!distance_MZ!unit=$mz_max_difference_unit
+#if $advanced.specify
+algorithm!distance_RT!weight=$advanced.rt_weight
+algorithm!distance_MZ!weight=$advanced.mz_weight
+algorithm!distance_intensity!weight=$advanced.intensity_weight
+algorithm!distance_RT!exponent=$advanced.rt_exponent
+algorithm!distance_MZ!exponent=$advanced.mz_exponent
+algorithm!distance_intensity!exponent=$advanced.intensity_exponent
+#end if
 </configfile>
   </configfiles>
   <inputs>
-    <conditional name="type">
-      <param name="input_type" type="select" label="Input Type">
-        <option value="featurexml">Features (FeatureXML)</option>
-        <option value="consensusxml">Consensus (ConsensusXML)</option>
-      </param>
-      <when value="featurexml">
-        <param format="featurexml" name="input1" type="data" label="Input Features" />
-      </when>
-      <when value="consensusxml">
-        <param format="consensusxml" name="input1" type="data" label="Input Consensus" />
-      </when>
-    </conditional>
+    <expand macro="feature_linker_input" />
+    <param name="second_nearest_gap" value="2" type="integer" label="Second Nearest Gap" help="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." />
+    <expand macro="feature_linker_algorithm_options" />
   </inputs>
   <outputs>
     <data format="consensusxml" name="output" />