--- a/macros.xml	Fri May 10 17:31:59 2013 -0400
+++ b/macros.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -80,4 +80,64 @@
       </change_format>
     </data>
   </macro>
+  <macro name="aligner_model">
+    <conditional name="model">
+      <param name="model_type" type="select" label="Model Type">
+        <option value="linear">Linear</option>
+        <option value="b_spline" selected="true">Smoothing spline (non-linear)</option>
+        <option value="interpolated">Interpolated</option>
+      </param>
+      <when value="linear">
+        <!-- TODO: Add symmetric_regression -->
+      </when>
+      <when value="b_spline">
+        <!-- TODO: Add num_breakpoints, break_positions -->
+      </when>
+      <when value="interpolated">
+        <param name="interpolation_type" type="select" label="Interpolation Type">
+          <option value="cspline" selected="true">cspline</option>
+          <option value="linear">linear</option>
+          <option value="akima">akima</option>
+        </param>
+      </when>
+    </conditional>
+  </macro>
+  <macro name="feature_linker_input">
+    <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="inputs" type="data" label="Input Features" multiple="true" />
+      </when>
+      <when value="consensusxml">
+        <param format="consensusxml" name="inputs" type="data" label="Input Consensus" multiple="true" />
+        <param name="keep_subelements" type="boolean" label="Transfer sub-features of the inputs to the output." truevalue="keep_subelements=true" falsevalue="" />        
+      </when>
+    </conditional>
+  </macro>
+  <macro name="feature_linker_algorithm_options">
+    <param name="use_identifications" type="boolean" truevalue="algorithm!use_identifications=true" falsevalue="" label="Use Identifications" checked="false" help="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." />
+    <param name="ignore_charge" type="boolean" truevalue="algorithm!ignore_charge=true" falsevalue="" label="Use Charge" help="Compare features normally even if their charge states are different." checked="false" />    
+    <param name="rt_max_difference" type="float" label="Max Difference (RT)" value="100" help="Maximum allowed difference in RT in seconds." />
+    <param name="mz_max_difference" type="float" label="Max Difference (m/z)" value="0.3" help="Maximum allowed difference in m/z" />
+    <param name="mz_max_difference_unit" type="select" label="Max Difference Units (m/z)">
+      <option value="Da" selected="true">Da</option>
+      <option value="ppm" selected="true">ppm</option>
+    </param>
+    <conditional name="advanced">
+      <param name="specify" type="boolean" label="Specify advanced exponents and weights for distances (RT, m/z, and intensity)" />
+      <when value="true">
+        <param name="rt_exponent" label="RT Exponent" help="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
+        <param name="mz_exponent" label="m/z Exponent" help="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
+        <param name="intensity_exponent" label="Intensity Exponent" help="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
+        <param name="rt_weight" label="RT Exponent" help="RT distances are weighted by this factor" type="float" value="1" />
+        <param name="mz_weight" label="m/z Exponent" help="m/z distances are weighted by this factor" type="float" value="2" />
+        <param name="intensity_weight" label="Intensity Exponent" help="Distances based on relative intensity are weighted by this factor" type="float" value="0" />
+      </when>
+      <when value="false">
+      </when>
+    </conditional>
+  </macro>
 </macros>
\ No newline at end of file