--- a/silac_analyzer.xml	Fri May 10 17:31:59 2013 -0400
+++ b/silac_analyzer.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -27,7 +27,6 @@
   </configfiles>
   <inputs>
     <param name="input1" type="data" format="mzml" label="Input peak list" />
-    <!-- TODO -->
     <param name="labels" type="select" multiple="true" label="Labels">
       <option value="Arg6" >Arg6</option>
       <option value="Arg10">Arg10</option>
@@ -46,17 +45,6 @@
     </param>
     <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" />
     <expand macro="raw_feature_finder_params" />
-    <!--
-    <param name="rt_threshold" type="float" value="50" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
-    <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
-    <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
-    <param name="intensity_correlation" type="float" value="0.9" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
-    <param name="model_deviation" type="float" value="6" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) &lt; observed_ratio &lt; ( theoretic_ratio * model_deviation )." />
-    <param name="min_charge" type="integer" value="1" label="Minimum Charge" />
-    <param name="max_charge" type="integer" value="5" label="Maximum Charge" />
-    <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
-    <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
-    -->
   </inputs>
   <outputs>
     <data format="consensusxml" name="out" />