--- a/SpectraMerger.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/SpectraMerger.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,62 +1,178 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="SpectraMerger" name="SpectraMerger" version="1.12.0">
-  <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
-  <macros>
-    <token name="@EXECUTABLE@">SpectraMerger</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>SpectraMerger
+<?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: [Signal processing and preprocessing]-->
+  <tool id="SpectraMerger" name="SpectraMerger" version="2.0.0">
+    <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
+    <macros>
+      <token name="@EXECUTABLE@">SpectraMerger</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>SpectraMerger
 
--in ${param_in}
--out ${param_out}
--merging_method ${param_merging_method}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:block_method:ms_levels ${param_ms_levels}
--algorithm:block_method:rt_block_size ${param_rt_block_size}
--algorithm:block_method:rt_max_length ${param_rt_max_length}
--algorithm:precursor_method:mz_tolerance ${param_mz_tolerance}
--algorithm:precursor_method:rt_tolerance ${param_rt_tolerance}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_merging_method:
+  -merging_method
+  #if &quot; &quot; in str($param_merging_method):
+    &quot;$param_merging_method&quot;
+  #else
+    $param_merging_method
+  #end if
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_average_gaussian_spectrum_type:
+  -algorithm:average_gaussian:spectrum_type
+  #if &quot; &quot; in str($param_algorithm_average_gaussian_spectrum_type):
+    &quot;$param_algorithm_average_gaussian_spectrum_type&quot;
+  #else
+    $param_algorithm_average_gaussian_spectrum_type
+  #end if
+#end if
+#if $param_algorithm_average_gaussian_ms_level:
+  -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
+#end if
+#if $param_algorithm_average_gaussian_rt_FWHM:
+  -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
+#end if
+#if $param_algorithm_average_tophat_spectrum_type:
+  -algorithm:average_tophat:spectrum_type
+  #if &quot; &quot; in str($param_algorithm_average_tophat_spectrum_type):
+    &quot;$param_algorithm_average_tophat_spectrum_type&quot;
+  #else
+    $param_algorithm_average_tophat_spectrum_type
+  #end if
+#end if
+#if $param_algorithm_average_tophat_ms_level:
+  -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
+#end if
+#if $param_algorithm_average_tophat_rt_range:
+  -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
+#end if
+#if $param_algorithm_average_tophat_rt_unit:
+  -algorithm:average_tophat:rt_unit
+  #if &quot; &quot; in str($param_algorithm_average_tophat_rt_unit):
+    &quot;$param_algorithm_average_tophat_rt_unit&quot;
+  #else
+    $param_algorithm_average_tophat_rt_unit
+  #end if
+#end if
+
+#if $rep_param_algorithm_block_method_ms_levels:
+-algorithm:block_method:ms_levels
+  #for token in $rep_param_algorithm_block_method_ms_levels:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_algorithm_block_method_ms_levels&quot;
+    #else
+      $token.param_algorithm_block_method_ms_levels
+    #end if
+  #end for
+#end if
+#if $param_algorithm_block_method_rt_block_size:
+  -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
+#end if
+#if $param_algorithm_block_method_rt_max_length:
+  -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
+#end if
+#if $param_algorithm_precursor_method_mz_tolerance:
+  -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
+#end if
+#if $param_algorithm_precursor_method_rt_tolerance:
+  -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width}
-    -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit}
-    -algorithm:sort_blocks ${adv_opts.param_sort_blocks}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_mz_binning_width:
+  -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
+#end if
+    #if $adv_opts.param_algorithm_mz_binning_width_unit:
+  -algorithm:mz_binning_width_unit
+  #if &quot; &quot; in str($adv_opts.param_algorithm_mz_binning_width_unit):
+    &quot;$adv_opts.param_algorithm_mz_binning_width_unit&quot;
+  #else
+    $adv_opts.param_algorithm_mz_binning_width_unit
+  #end if
+#end if
+    #if $adv_opts.param_algorithm_sort_blocks:
+  -algorithm:sort_blocks
+  #if &quot; &quot; in str($adv_opts.param_algorithm_sort_blocks):
+    &quot;$adv_opts.param_algorithm_sort_blocks&quot;
+  #else
+    $adv_opts.param_algorithm_sort_blocks
+  #end if
+#end if
+    #if $adv_opts.param_algorithm_average_gaussian_cutoff:
+  -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file." help="(-in)"/>
-    <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used." help="(-merging_method)">
-      <option value="precursor_method">precursor_method</option>
-      <option value="block_method">block_method</option>
-    </param>
-    <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1" label="Merge spectra of this level. All spectra with other MS levels remain untouched." help="(-ms_levels)"/>
-    <param name="param_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up." help="(-rt_block_size)"/>
-    <param name="param_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)." help="(-rt_max_length)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]." help="(-mz_tolerance)"/>
-    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]." help="(-rt_tolerance)"/>
-    <expand macro="advanced_options">
-      <param name="param_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged." help="(-mz_binning_width)"/>
-      <param name="param_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given." help="(-mz_binning_width_unit)">
-        <option value="Da">Da</option>
-        <option value="ppm">ppm</option>
+    <inputs>
+      <param format="mzml" help="(-in) " label="Input mzML file" name="param_in" optional="False" type="data"/>
+      <param help="(-merging_method) " label="Method of merging which should be used" name="param_merging_method" optional="True" type="select" value="average_gaussian">
+        <option value="average_gaussian">average_gaussian</option>
+        <option value="average_tophat">average_tophat</option>
+        <option value="precursor_method">precursor_method</option>
+        <option value="block_method">block_method</option>
+      </param>
+      <param help="(-spectrum_type) " label="Spectrum type of the MS level to be averaged" name="param_algorithm_average_gaussian_spectrum_type" optional="True" type="select" value="automatic">
+        <option value="profile">profile</option>
+        <option value="centroid">centroid</option>
+        <option value="automatic">automatic</option>
+      </param>
+      <param help="(-ms_level) All other spectra remain unchanged" label="Average spectra of this level" min="1" name="param_algorithm_average_gaussian_ms_level" optional="True" type="integer" value="1"/>
+      <param help="(-rt_FWHM) " label="FWHM of Gauss curve in seconds to be averaged ove" max="1e+11" min="0.0" name="param_algorithm_average_gaussian_rt_FWHM" optional="True" type="float" value="5.0"/>
+      <param help="(-spectrum_type) " label="Spectrum type of the MS level to be averaged" name="param_algorithm_average_tophat_spectrum_type" optional="True" type="select" value="automatic">
+        <option value="profile">profile</option>
+        <option value="centroid">centroid</option>
+        <option value="automatic">automatic</option>
+      </param>
+      <param help="(-ms_level) All other spectra remain unchanged" label="Average spectra of this level" min="1" name="param_algorithm_average_tophat_ms_level" optional="True" type="integer" value="1"/>
+      <param help="(-rt_range) +/-(RT range)/2 from each spectrum" label="RT range to be averaged over, i.e" max="1e+11" min="0.0" name="param_algorithm_average_tophat_rt_range" optional="True" type="float" value="5.0"/>
+      <param help="(-rt_unit) " label="Unit for RT range" name="param_algorithm_average_tophat_rt_unit" optional="True" type="select" value="scans">
+        <option value="scans">scans</option>
+        <option value="seconds">seconds</option>
       </param>
-      <param name="param_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks)">
-        <option value="RT_ascending">RT_ascending</option>
-        <option value=" RT_descending"> RT_descending</option>
-      </param>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output mzML file with merged spectra." format="mzML"/>
-  </outputs>
-  <help>**What it does**
-
-Merges spectra (each MS level separately), increasing S/N ratios.
+      <repeat max="1" min="0" name="rep_param_algorithm_block_method_ms_levels" title="param_algorithm_block_method_ms_levels">
+        <param help="(-ms_levels) All spectra with other MS levels remain untouched" label="Merge spectra of this level" min="1" name="param_algorithm_block_method_ms_levels" optional="True" size="30" type="text" value="1">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-rt_block_size) " label="Maximum number of scans to be summed up" min="1" name="param_algorithm_block_method_rt_block_size" optional="True" type="integer" value="5"/>
+      <param help="(-rt_max_length) " label="Maximum RT size of the block in seconds (0.0 = no size restriction)" max="1e+11" min="0.0" name="param_algorithm_block_method_rt_max_length" optional="True" type="float" value="0.0"/>
+      <param help="(-mz_tolerance) " label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" min="0.0" name="param_algorithm_precursor_method_mz_tolerance" optional="True" type="float" value="0.0001"/>
+      <param help="(-rt_tolerance) " label="Max RT distance of the precursor entries of two spectra to be merged in [s]" min="0.0" name="param_algorithm_precursor_method_rt_tolerance" optional="True" type="float" value="5.0"/>
+      <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="(-mz_binning_width) Closer data points or peaks will be merged" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" min="0.0" name="param_algorithm_mz_binning_width" optional="True" type="float" value="5.0"/>
+        <param help="(-mz_binning_width_unit) " label="Unit in which the distance between two data points or peaks is given" name="param_algorithm_mz_binning_width_unit" optional="True" type="select" value="ppm">
+          <option value="Da">Da</option>
+          <option value="ppm">ppm</option>
+        </param>
+        <param help="(-sort_blocks) " label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" name="param_algorithm_sort_blocks" optional="True" type="select" value="RT_ascending">
+          <option value="RT_ascending">RT_ascending</option>
+          <option value=" RT_descending"> RT_descending</option>
+        </param>
+        <param help="(-cutoff) The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average" label="Intensity cutoff for Gaussian" max="1.0" min="0.0" name="param_algorithm_average_gaussian_cutoff" optional="True" type="float" value="0.01"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="mzml" name="param_out"/>
+    </outputs>
+    <help>Merges spectra (each MS level separately), increasing S/N ratios.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help>
+  </tool>