--- a/NoiseFilterGaussian.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/NoiseFilterGaussian.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,38 +1,65 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="1.12.0">
-  <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
+<?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="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="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>NoiseFilterGaussian
 
--in ${param_in}
--out ${param_out}
--processOption inmemory
--threads \${GALAXY_SLOTS:-24} 
--algorithm:gaussian_width ${param_gaussian_width}
--algorithm:ppm_tolerance ${param_ppm_tolerance}
-${param_use_ppm_tolerance}
+#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 $adv_opts.param_processOption:
+  -processOption
+  #if &quot; &quot; in str($adv_opts.param_processOption):
+    &quot;$adv_opts.param_processOption&quot;
+  #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_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_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position.#br#The higher the value, the wider the peak and therefore the wider the gaussian." help="(-ppm_tolerance)"/>
-    <param name="param_use_ppm_tolerance" type="boolean" truevalue="-algorithm:use_ppm_tolerance true" falsevalue="-algorithm:use_ppm_tolerance false" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower." help="(-use_ppm_tolerance)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output raw data file " format="mzML"/>
-  </outputs>
-  <help>**What it does**
-
-Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
+    <inputs>
+      <param format="mzml" help="(-in) " label="input raw data file" name="param_in" optional="False" type="data"/>
+      <param help="(-gaussian_width) " label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" name="param_algorithm_gaussian_width" type="float" value="0.2"/>
+      <param help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian" label="Gaussian width, depending on the m/z position" name="param_algorithm_ppm_tolerance" type="float" value="10.0"/>
+      <param checked="false" falsevalue="" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" name="param_algorithm_use_ppm_tolerance" optional="True" truevalue="-algorithm:use_ppm_tolerance" type="boolean"/>
+      <expand macro="advanced_options">
+        <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory">
+          <option value="inmemory">inmemory</option>
+          <option value="lowmemory">lowmemory</option>
+        </param>
+        <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="mzml" name="param_out"/>
+    </outputs>
+    <help>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
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
+  </tool>