--- a/FeatureFinderSuperHirn.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FeatureFinderSuperHirn.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,87 +1,170 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="1.12.0">
-  <description>Finds mass spectrometric features in mass spectra.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FeatureFinderSuperHirn
+<?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="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.0.0">
+    <description>Finds mass spectrometric features in mass spectra.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FeatureFinderSuperHirn
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_centroiding_active:
+  -algorithm:centroiding:active
+#end if
+#if $param_algorithm_centroiding_window_width:
+  -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
+#end if
+#if $param_algorithm_centroiding_absolute_isotope_mass_precision:
+  -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
+#end if
+#if $param_algorithm_centroiding_relative_isotope_mass_precision:
+  -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
+#end if
+#if $param_algorithm_centroiding_minimal_peak_height:
+  -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
+#end if
+#if $param_algorithm_centroiding_min_ms_signal_intensity:
+  -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
+#end if
 
--in ${param_in}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
-${param_active}
--algorithm:centroiding:window_width ${param_window_width}
--algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision}
--algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision}
--algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height}
--algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity}
--algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels}
--algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance}
--algorithm:ms1:tr_resolution ${param_tr_resolution}
--algorithm:ms1:intensity_threshold ${param_intensity_threshold}
--algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance}
--algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members}
--algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor}
--algorithm:ms1:intensity_cv ${param_intensity_cv}
--algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance}
--algorithm:ms1:mz_tolerance ${param_mz_tolerance}
-${param_active}
--algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution}
--algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance}
--algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance}
--algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage}
--algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering}
--algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window}
--algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window}
--algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min}
--algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max}
--algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min}
--algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max}
+#if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
+-algorithm:ms1:precursor_detection_scan_levels
+  #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_algorithm_ms1_precursor_detection_scan_levels&quot;
+    #else
+      $token.param_algorithm_ms1_precursor_detection_scan_levels
+    #end if
+  #end for
+#end if
+#if $param_algorithm_ms1_max_inter_scan_distance:
+  -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
+#end if
+#if $param_algorithm_ms1_tr_resolution:
+  -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
+#end if
+#if $param_algorithm_ms1_intensity_threshold:
+  -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
+#end if
+#if $param_algorithm_ms1_max_inter_scan_rt_distance:
+  -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
+#end if
+#if $param_algorithm_ms1_min_nb_cluster_members:
+  -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
+#end if
+#if $param_algorithm_ms1_detectable_isotope_factor:
+  -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
+#end if
+#if $param_algorithm_ms1_intensity_cv:
+  -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
+#end if
+#if $param_algorithm_ms1_retention_time_tolerance:
+  -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
+#end if
+#if $param_algorithm_ms1_mz_tolerance:
+  -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
+#end if
+#if $param_algorithm_ms1_feature_merger_active:
+  -algorithm:ms1_feature_merger:active
+#end if
+#if $param_algorithm_ms1_feature_merger_tr_resolution:
+  -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
+#end if
+#if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
+  -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
+#end if
+#if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
+  -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
+#end if
+#if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
+  -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
+#end if
+#if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
+  -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
+#end if
+#if $param_algorithm_ms1_feature_selection_options_start_elution_window:
+  -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
+#end if
+#if $param_algorithm_ms1_feature_selection_options_end_elution_window:
+  -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
+#end if
+#if $param_algorithm_ms1_feature_selection_options_mz_range_min:
+  -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
+#end if
+#if $param_algorithm_ms1_feature_selection_options_mz_range_max:
+  -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
+#end if
+#if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
+  -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
+#end if
+#if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
+  -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/>
-    <param name="param_active" type="boolean" truevalue="-algorithm:centroiding:active true" falsevalue="-algorithm:centroiding:active false" checked="false" optional="True" label="MS1 data centroid data" help="(-active)"/>
-    <param name="param_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width)"/>
-    <param name="param_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision)"/>
-    <param name="param_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision)"/>
-    <param name="param_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height)"/>
-    <param name="param_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity)"/>
-    <param name="param_precursor_detection_scan_levels" type="text" size="20" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels)"/>
-    <param name="param_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance)"/>
-    <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
-    <param name="param_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold)"/>
-    <param name="param_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance)"/>
-    <param name="param_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members)"/>
-    <param name="param_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope factor" help="(-detectable_isotope_factor)"/>
-    <param name="param_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv)"/>
-    <param name="param_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance)"/>
-    <param name="param_active" type="boolean" truevalue="-algorithm:ms1_feature_merger:active true" falsevalue="-algorithm:ms1_feature_merger:active false" checked="true" optional="True" label="Activation of MS1 feature merging post processing" help="(-active)"/>
-    <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
-    <param name="param_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance)"/>
-    <param name="param_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance)"/>
-    <param name="param_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage)"/>
-    <param name="param_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering)"/>
-    <param name="param_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window)"/>
-    <param name="param_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window)"/>
-    <param name="param_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min)"/>
-    <param name="param_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max)"/>
-    <param name="param_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min)"/>
-    <param name="param_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output peak file " format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Finds mass spectrometric features in mass spectra.
+    <inputs>
+      <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-active) " label="MS1 data centroid data" name="param_algorithm_centroiding_active" optional="True" truevalue="-algorithm:centroiding:active" type="boolean"/>
+      <param help="(-window_width) " label="Centroid window width" min="1" name="param_algorithm_centroiding_window_width" optional="True" type="integer" value="5"/>
+      <param help="(-absolute_isotope_mass_precision) " label="Absolute isotope mass precision (Da)" min="0.0" name="param_algorithm_centroiding_absolute_isotope_mass_precision" optional="True" type="float" value="0.01"/>
+      <param help="(-relative_isotope_mass_precision) " label="Relative isotope mass precision" min="0.0" name="param_algorithm_centroiding_relative_isotope_mass_precision" optional="True" type="float" value="10.0"/>
+      <param help="(-minimal_peak_height) " label="Minimal peak height" min="0.0" name="param_algorithm_centroiding_minimal_peak_height" optional="True" type="float" value="0.0"/>
+      <param help="(-min_ms_signal_intensity) " label="Minimal Centroid MS Signal Intensity" min="0.0" name="param_algorithm_centroiding_min_ms_signal_intensity" optional="True" type="float" value="50.0"/>
+      <repeat max="1" min="0" name="rep_param_algorithm_ms1_precursor_detection_scan_levels" title="param_algorithm_ms1_precursor_detection_scan_levels">
+        <param help="(-precursor_detection_scan_levels) " label="Precursor detection scan levels" name="param_algorithm_ms1_precursor_detection_scan_levels" size="30" type="text" value="1">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-max_inter_scan_distance) " label="MS1 max inter scan distance" min="0" name="param_algorithm_ms1_max_inter_scan_distance" optional="True" type="integer" value="0"/>
+      <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_tr_resolution" optional="True" type="float" value="0.01"/>
+      <param help="(-intensity_threshold) " label="FT peak detect MS1 intensity min threshold" min="0.0" name="param_algorithm_ms1_intensity_threshold" optional="True" type="float" value="1000.0"/>
+      <param help="(-max_inter_scan_rt_distance) " label="MS1 max inter scan distance" min="0.0" name="param_algorithm_ms1_max_inter_scan_rt_distance" optional="True" type="float" value="0.1"/>
+      <param help="(-min_nb_cluster_members) " label="FT peak detect MS1 min nb peak members" min="0" name="param_algorithm_ms1_min_nb_cluster_members" optional="True" type="integer" value="4"/>
+      <param help="(-detectable_isotope_factor) " label="Detectable isotope facto" min="0.0" name="param_algorithm_ms1_detectable_isotope_factor" optional="True" type="float" value="0.05"/>
+      <param help="(-intensity_cv) " label="IntensityCV" min="0.0" name="param_algorithm_ms1_intensity_cv" optional="True" type="float" value="0.9"/>
+      <param help="(-retention_time_tolerance) " label="MS1 retention time tolerance (minutes)" min="0.0" name="param_algorithm_ms1_retention_time_tolerance" optional="True" type="float" value="0.5"/>
+      <param help="(-mz_tolerance) " label="MS1 m/z tolerance (ppm)" min="0.0" name="param_algorithm_ms1_mz_tolerance" optional="True" type="float" value="0.0"/>
+      <param checked="true" falsevalue="" help="(-active) " label="Activation of MS1 feature merging post processing" name="param_algorithm_ms1_feature_merger_active" optional="True" truevalue="-algorithm:ms1_feature_merger:active" type="boolean"/>
+      <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_feature_merger_tr_resolution" optional="True" type="float" value="0.01"/>
+      <param help="(-initial_apex_tr_tolerance) " label="Initial Apex Tr tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" optional="True" type="float" value="5.0"/>
+      <param help="(-feature_merging_tr_tolerance) " label="MS1 feature Tr merging tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" optional="True" type="float" value="1.0"/>
+      <param help="(-intensity_variation_percentage) " label="Percentage of intensity variation between LC border peaks" max="100.0" min="0.0" name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" optional="True" type="float" value="25.0"/>
+      <param help="(-ppm_tolerance_for_mz_clustering) " label="PPM value for the m/z clustering of merging candidates" min="0.0" name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" optional="True" type="float" value="10.0"/>
+      <param help="(-start_elution_window) " label="start elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_start_elution_window" optional="True" type="float" value="0.0"/>
+      <param help="(-end_elution_window) " label="end elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_end_elution_window" optional="True" type="float" value="180.0"/>
+      <param help="(-mz_range_min) " label="MS1 feature mz range min" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_min" optional="True" type="float" value="0.0"/>
+      <param help="(-mz_range_max) " label="MS1 feature mz range max" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_max" optional="True" type="float" value="2000.0"/>
+      <param help="(-chrg_range_min) " label="MS1 feature CHRG range min" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_min" optional="True" type="integer" value="1"/>
+      <param help="(-chrg_range_max) " label="MS1 feature CHRG range max" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_max" optional="True" type="integer" value="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"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>Finds mass spectrometric features in mass spectra.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html</help>
+  </tool>