--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NoiseFilterGaussian.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,65 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.0.0">
+  <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
+  <macros>
+    <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>NoiseFilterGaussian
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_algorithm_gaussian_width:
+  -algorithm:gaussian_width $param_algorithm_gaussian_width
+#end if
+#if $param_algorithm_ppm_tolerance:
+  -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
+#end if
+#if $param_algorithm_use_ppm_tolerance:
+  -algorithm:use_ppm_tolerance
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_processOption:
+  -processOption
+  #if " " in str($adv_opts.param_processOption):
+    "$adv_opts.param_processOption"
+  #else
+    $adv_opts.param_processOption
+  #end if
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
+    <param name="param_algorithm_gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help="(-gaussian_width) "/>
+    <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian"/>
+    <param name="param_algorithm_use_ppm_tolerance" type="boolean" truevalue="-algorithm:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower"/>
+    <expand macro="advanced_options">
+      <param name="param_processOption" type="select" optional="True" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) ">
+        <option value="inmemory">inmemory</option>
+        <option value="lowmemory">lowmemory</option>
+      </param>
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzml"/>
+  </outputs>
+  <help>**What it does**
+
+Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
+  <expand macro="references"/>
+</tool>