--- a/FeatureFinderCentroided.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FeatureFinderCentroided.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,102 +1,178 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="1.12.0">
-  <description>Detects two-dimensional features in LC-MS data.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FeatureFinderCentroided
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Quantitation]-->
+  <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.0.0">
+    <description>Detects two-dimensional features in LC-MS data.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FeatureFinderCentroided
 
--in ${param_in}
--out ${param_out}
--seeds ${param_seeds}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:intensity:bins ${param_bins}
--algorithm:mass_trace:mz_tolerance ${param_mz_tolerance}
--algorithm:mass_trace:min_spectra ${param_min_spectra}
--algorithm:mass_trace:max_missing ${param_max_missing}
--algorithm:mass_trace:slope_bound ${param_slope_bound}
--algorithm:isotopic_pattern:charge_low ${param_charge_low}
--algorithm:isotopic_pattern:charge_high ${param_charge_high}
--algorithm:isotopic_pattern:mz_tolerance ${param_mz_tolerance}
--algorithm:seed:min_score ${param_min_score}
--algorithm:feature:min_score ${param_min_score}
--algorithm:feature:reported_mz ${param_reported_mz}
--algorithm:user-seed:rt_tolerance ${param_rt_tolerance}
--algorithm:user-seed:mz_tolerance ${param_mz_tolerance}
--algorithm:user-seed:min_score ${param_min_score}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_seeds:
+  -seeds $param_seeds
+#end if
+#if $param_out_mzq:
+  -out_mzq $param_out_mzq
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_intensity_bins:
+  -algorithm:intensity:bins $param_algorithm_intensity_bins
+#end if
+#if $param_algorithm_mass_trace_mz_tolerance:
+  -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance
+#end if
+#if $param_algorithm_mass_trace_min_spectra:
+  -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra
+#end if
+#if $param_algorithm_mass_trace_max_missing:
+  -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing
+#end if
+#if $param_algorithm_mass_trace_slope_bound:
+  -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound
+#end if
+#if $param_algorithm_isotopic_pattern_charge_low:
+  -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low
+#end if
+#if $param_algorithm_isotopic_pattern_charge_high:
+  -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high
+#end if
+#if $param_algorithm_isotopic_pattern_mz_tolerance:
+  -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance
+#end if
+#if $param_algorithm_seed_min_score:
+  -algorithm:seed:min_score $param_algorithm_seed_min_score
+#end if
+#if $param_algorithm_feature_min_score:
+  -algorithm:feature:min_score $param_algorithm_feature_min_score
+#end if
+#if $param_algorithm_feature_reported_mz:
+  -algorithm:feature:reported_mz
+  #if &quot; &quot; in str($param_algorithm_feature_reported_mz):
+    &quot;$param_algorithm_feature_reported_mz&quot;
+  #else
+    $param_algorithm_feature_reported_mz
+  #end if
+#end if
+#if $param_algorithm_user_seed_rt_tolerance:
+  -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
+#end if
+#if $param_algorithm_user_seed_mz_tolerance:
+  -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance
+#end if
+#if $param_algorithm_user_seed_min_score:
+  -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -out_mzq ${adv_opts.param_out_mzq}
-    -algorithm:debug:pseudo_rt_shift ${adv_opts.param_pseudo_rt_shift}
-    -algorithm:isotopic_pattern:intensity_percentage ${adv_opts.param_intensity_percentage}
-    -algorithm:isotopic_pattern:intensity_percentage_optional ${adv_opts.param_intensity_percentage_optional}
-    -algorithm:isotopic_pattern:optional_fit_improvement ${adv_opts.param_optional_fit_improvement}
-    -algorithm:isotopic_pattern:mass_window_width ${adv_opts.param_mass_window_width}
-    -algorithm:isotopic_pattern:abundance_12C ${adv_opts.param_abundance_12C}
-    -algorithm:isotopic_pattern:abundance_14N ${adv_opts.param_abundance_14N}
-    -algorithm:fit:max_iterations ${adv_opts.param_max_iterations}
-    -algorithm:feature:min_isotope_fit ${adv_opts.param_min_isotope_fit}
-    -algorithm:feature:min_trace_score ${adv_opts.param_min_trace_score}
-    -algorithm:feature:min_rt_span ${adv_opts.param_min_rt_span}
-    -algorithm:feature:max_rt_span ${adv_opts.param_max_rt_span}
-    -algorithm:feature:rt_shape ${adv_opts.param_rt_shape}
-    -algorithm:feature:max_intersection ${adv_opts.param_max_intersection}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_debug_pseudo_rt_shift:
+  -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage:
+  -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional:
+  -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement:
+  -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width:
+  -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C:
+  -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C
+#end if
+    #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N:
+  -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N
+#end if
+    #if $adv_opts.param_algorithm_fit_max_iterations:
+  -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations
+#end if
+    #if $adv_opts.param_algorithm_feature_min_isotope_fit:
+  -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit
+#end if
+    #if $adv_opts.param_algorithm_feature_min_trace_score:
+  -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score
+#end if
+    #if $adv_opts.param_algorithm_feature_min_rt_span:
+  -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span
+#end if
+    #if $adv_opts.param_algorithm_feature_max_rt_span:
+  -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
+#end if
+    #if $adv_opts.param_algorithm_feature_rt_shape:
+  -algorithm:feature:rt_shape
+  #if &quot; &quot; in str($adv_opts.param_algorithm_feature_rt_shape):
+    &quot;$adv_opts.param_algorithm_feature_rt_shape&quot;
+  #else
+    $adv_opts.param_algorithm_feature_rt_shape
+  #end if
+#end if
+    #if $adv_opts.param_algorithm_feature_max_intersection:
+  -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/>
-    <param name="param_seeds" type="data" format="featureXML" optional="True" label="User specified seed list" help="(-seeds)"/>
-    <param name="param_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." help="(-bins)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
-    <param name="param_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace." help="(-min_spectra)"/>
-    <param name="param_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" help="(-max_missing)"/>
-    <param name="param_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." help="(-slope_bound)"/>
-    <param name="param_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search for." help="(-charge_low)"/>
-    <param name="param_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search for." help="(-charge_high)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
-    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." help="(-min_score)"/>
-    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." help="(-min_score)"/>
-    <param name="param_reported_mz" type="select" optional="True" value="monoisotopic" label="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." help="(-reported_mz)">
-      <option value="maximum">maximum</option>
-      <option value="average">average</option>
-      <option value="monoisotopic">monoisotopic</option>
-    </param>
-    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position." help="(-rt_tolerance)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position." help="(-mz_tolerance)"/>
-    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." help="(-min_score)"/>
-    <expand macro="advanced_options">
-      <param name="param_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when ." help="(-pseudo_rt_shift)"/>
-      <param name="param_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." help="(-intensity_percentage)"/>
-      <param name="param_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." help="(-intensity_percentage_optional)"/>
-      <param name="param_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak." help="(-optional_fit_improvement)"/>
-      <param name="param_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions." help="(-mass_window_width)"/>
-      <param name="param_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel. abundance of the light carbon. Modify if labeled." help="(-abundance_12C)"/>
-      <param name="param_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel. abundance of the light nitrogen. Modify if labeled." help="(-abundance_14N)"/>
-      <param name="param_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit." help="(-max_iterations)"/>
-      <param name="param_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting." help="(-min_isotope_fit)"/>
-      <param name="param_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." help="(-min_trace_score)"/>
-      <param name="param_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting." help="(-min_rt_span)"/>
-      <param name="param_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have." help="(-max_rt_span)"/>
-      <param name="param_rt_shape" type="select" optional="True" value="symmetric" label="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." help="(-rt_shape)">
-        <option value="symmetric">symmetric</option>
-        <option value="asymmetric">asymmetric</option>
+    <inputs>
+      <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param format="xml" help="(-seeds) " label="User specified seed list" name="param_seeds" optional="True" type="data"/>
+      <param help="(-bins) The higher this value, the more local the intensity significance score is. &lt;br&gt;This parameter should be decreased, if the algorithm is used on small regions of a map" label="Number of bins per dimension (RT and m/z)" min="1" name="param_algorithm_intensity_bins" optional="True" type="integer" value="10"/>
+      <param help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!" label="Tolerated m/z deviation of peaks belonging to the same mass trace" min="0.0" name="param_algorithm_mass_trace_mz_tolerance" optional="True" type="float" value="0.03"/>
+      <param help="(-min_spectra) " label="Number of spectra that have to show a similar peak mass in a mass trace" min="1" name="param_algorithm_mass_trace_min_spectra" optional="True" type="integer" value="10"/>
+      <param help="(-max_missing) &lt;br&gt;This parameter should be well below 'min_spectra'!" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" min="0" name="param_algorithm_mass_trace_max_missing" optional="True" type="integer" value="1"/>
+      <param help="(-slope_bound) &lt;br&gt;This parameter is important to seperate overlapping elution peaks. &lt;br&gt;It should be increased if feature elution profiles fluctuate a lot" label="The maximum slope of mass trace intensities when extending from the highest peak" min="0.0" name="param_algorithm_mass_trace_slope_bound" optional="True" type="float" value="0.1"/>
+      <param help="(-charge_low) " label="Lowest charge to search fo" min="1" name="param_algorithm_isotopic_pattern_charge_low" optional="True" type="integer" value="1"/>
+      <param help="(-charge_high) " label="Highest charge to search fo" min="1" name="param_algorithm_isotopic_pattern_charge_high" optional="True" type="integer" value="4"/>
+      <param help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!" label="Tolerated m/z deviation from the theoretical isotopic pattern" min="0.0" name="param_algorithm_isotopic_pattern_mz_tolerance" optional="True" type="float" value="0.03"/>
+      <param help="(-min_score) &lt;br&gt;The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. &lt;br&gt;If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score" label="Minimum seed score a peak has to reach to be used as seed" max="1.0" min="0.0" name="param_algorithm_seed_min_score" optional="True" type="float" value="0.8"/>
+      <param help="(-min_score) &lt;br&gt;The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks" label="Feature score threshold for a feature to be reported" max="1.0" min="0.0" name="param_algorithm_feature_min_score" optional="True" type="float" value="0.7"/>
+      <param help="(-reported_mz) &lt;br&gt;'maximum' returns the m/z value of the highest mass trace. &lt;br&gt;'average' returns the intensity-weighted average m/z value of all contained peaks. &lt;br&gt;'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model" label="The mass type that is reported for features" name="param_algorithm_feature_reported_mz" optional="True" type="select" value="monoisotopic">
+        <option value="maximum">maximum</option>
+        <option value="average">average</option>
+        <option value="monoisotopic">monoisotopic</option>
       </param>
-      <param name="param_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features." help="(-max_intersection)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="featureXML"/>
-    <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Detects two-dimensional features in LC-MS data.
+      <param help="(-rt_tolerance) " label="Allowed RT deviation of seeds from the user-specified seed position" min="0.0" name="param_algorithm_user_seed_rt_tolerance" optional="True" type="float" value="5.0"/>
+      <param help="(-mz_tolerance) " label="Allowed m/z deviation of seeds from the user-specified seed position" min="0.0" name="param_algorithm_user_seed_mz_tolerance" optional="True" type="float" value="1.1"/>
+      <param help="(-min_score) The cutoff is typically a bit lower in this case" label="Overwrites 'seed:min_score' for user-specified seeds" max="1.0" min="0.0" name="param_algorithm_user_seed_min_score" optional="True" type="float" value="0.5"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-pseudo_rt_shift) " label="Pseudo RT shift used when" min="1.0" name="param_algorithm_debug_pseudo_rt_shift" optional="True" type="float" value="500.0"/>
+        <param help="(-intensity_percentage) " label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" max="100.0" min="0.0" name="param_algorithm_isotopic_pattern_intensity_percentage" optional="True" type="float" value="10.0"/>
+        <param help="(-intensity_percentage_optional) " label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" max="100.0" min="0.0" name="param_algorithm_isotopic_pattern_intensity_percentage_optional" optional="True" type="float" value="0.1"/>
+        <param help="(-optional_fit_improvement) " label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" max="100.0" min="0.0" name="param_algorithm_isotopic_pattern_optional_fit_improvement" optional="True" type="float" value="2.0"/>
+        <param help="(-mass_window_width) " label="Window width in Dalton for precalculation of estimated isotope distributions" max="200.0" min="1.0" name="param_algorithm_isotopic_pattern_mass_window_width" optional="True" type="float" value="25.0"/>
+        <param help="(-abundance_12C) abundance of the light carbon. Modify if labeled" label="Rel" max="100.0" min="0.0" name="param_algorithm_isotopic_pattern_abundance_12C" optional="True" type="float" value="98.93"/>
+        <param help="(-abundance_14N) abundance of the light nitrogen. Modify if labeled" label="Rel" max="100.0" min="0.0" name="param_algorithm_isotopic_pattern_abundance_14N" optional="True" type="float" value="99.632"/>
+        <param help="(-max_iterations) " label="Maximum number of iterations of the fit" min="1" name="param_algorithm_fit_max_iterations" optional="True" type="integer" value="500"/>
+        <param help="(-min_isotope_fit) " label="Minimum isotope fit of the feature before model fitting" max="1.0" min="0.0" name="param_algorithm_feature_min_isotope_fit" optional="True" type="float" value="0.8"/>
+        <param help="(-min_trace_score) &lt;br&gt;Traces below this threshold are removed after the model fitting. &lt;br&gt;This parameter is important for features that overlap in m/z dimension" label="Trace score threshold" max="1.0" min="0.0" name="param_algorithm_feature_min_trace_score" optional="True" type="float" value="0.5"/>
+        <param help="(-min_rt_span) " label="Minimum RT span in relation to extended area that has to remain after model fitting" max="1.0" min="0.0" name="param_algorithm_feature_min_rt_span" optional="True" type="float" value="0.333"/>
+        <param help="(-max_rt_span) " label="Maximum RT span in relation to extended area that the model is allowed to have" min="0.5" name="param_algorithm_feature_max_rt_span" optional="True" type="float" value="2.5"/>
+        <param help="(-rt_shape) If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used" label="Choose model used for RT profile fitting" name="param_algorithm_feature_rt_shape" optional="True" type="select" value="symmetric">
+          <option value="symmetric">symmetric</option>
+          <option value="asymmetric">asymmetric</option>
+        </param>
+        <param help="(-max_intersection) " label="Maximum allowed intersection of features" max="1.0" min="0.0" name="param_algorithm_feature_max_intersection" optional="True" type="float" value="0.35"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+      <data format="mzq" name="param_out_mzq"/>
+    </outputs>
+    <help>Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help>
+  </tool>