--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraMerger.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,62 @@
+<?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
+
+-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 $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}
+#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>
+      </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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html
+
+@REFERENCES@
+</help>
+</tool>