--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraMerger.xml	Wed Mar 01 12:42:48 2017 -0500
@@ -0,0 +1,147 @@
+<?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="2.1.0">
+  <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
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_merging_method:
+  -merging_method $param_merging_method
+#end if
+#if $param_algorithm_average_gaussian_spectrum_type:
+  -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type
+#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 $param_algorithm_average_tophat_spectrum_type
+#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 $param_algorithm_average_tophat_rt_unit
+#end if
+
+#if $rep_param_algorithm_block_method_ms_levels:
+-algorithm:block_method:ms_levels
+  #for token in $rep_param_algorithm_block_method_ms_levels:
+    #if " " in str(token):
+      "$token.param_algorithm_block_method_ms_levels"
+    #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':
+    #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 $adv_opts.param_algorithm_mz_binning_width_unit
+#end if
+    #if $adv_opts.param_algorithm_sort_blocks:
+  -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks
+#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" display="radio" type="select" optional="False" value="average_gaussian" label="Method of merging which should be used" help="(-merging_method) ">
+      <option value="average_gaussian" selected="true">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 name="param_algorithm_average_gaussian_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
+      <option value="profile">profile</option>
+      <option value="centroid">centroid</option>
+      <option value="automatic" selected="true">automatic</option>
+    </param>
+    <param name="param_algorithm_average_gaussian_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
+    <param name="param_algorithm_average_gaussian_rt_FWHM" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help="(-rt_FWHM) "/>
+    <param name="param_algorithm_average_tophat_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
+      <option value="profile">profile</option>
+      <option value="centroid">centroid</option>
+      <option value="automatic" selected="true">automatic</option>
+    </param>
+    <param name="param_algorithm_average_tophat_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
+    <param name="param_algorithm_average_tophat_rt_range" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="RT range to be averaged over, i.e" help="(-rt_range) +/-(RT range)/2 from each spectrum"/>
+    <param name="param_algorithm_average_tophat_rt_unit" display="radio" type="select" optional="False" value="scans" label="Unit for RT range" help="(-rt_unit) ">
+      <option value="scans" selected="true">scans</option>
+      <option value="seconds">seconds</option>
+    </param>
+    <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels">
+      <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_algorithm_block_method_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_algorithm_block_method_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_algorithm_precursor_method_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_algorithm_precursor_method_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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="(-mz_binning_width) Closer data points or peaks will be merged"/>
+      <param name="param_algorithm_mz_binning_width_unit" display="radio" type="select" optional="False" value="ppm" label="Unit in which the distance between two data points or peaks is given" help="(-mz_binning_width_unit) ">
+        <option value="Da">Da</option>
+        <option value="ppm" selected="true">ppm</option>
+      </param>
+      <param name="param_algorithm_sort_blocks" display="radio" type="select" optional="False" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks) ">
+        <option value="RT_ascending" selected="true">RT_ascending</option>
+        <option value=" RT_descending"> RT_descending</option>
+      </param>
+      <param name="param_algorithm_average_gaussian_cutoff" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Intensity cutoff for Gaussian" 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"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzml"/>
+  </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</help>
+</tool>