--- a/NoiseFilterGaussian.xml	Fri Nov 06 19:42:03 2020 +0000
+++ b/NoiseFilterGaussian.xml	Thu Dec 01 19:19:06 2022 +0000
@@ -1,13 +1,11 @@
 <?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 CTDConverter.-->
 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
-<tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <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>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,21 +39,22 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" optional="true" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
       <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" optional="true" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
       <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/>
+      <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" 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="">
+      <param argument="-processOption" type="select" optional="true" 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="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="processOption"/>
       </param>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -68,13 +67,98 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_NoiseFilterGaussian"/>
-    <expand macro="manutest_NoiseFilterGaussian"/>
+  <tests><!-- TOPP_NoiseFilterGaussian_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="inmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
+      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="gaussian_width" value="1.0"/>
+        <param name="ppm_tolerance" value="10.0"/>
+        <param name="use_ppm_tolerance" value="false"/>
+        <param name="write_log_messages" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_NoiseFilterGaussian_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="inmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
+      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="gaussian_width" value="50.0"/>
+        <param name="ppm_tolerance" value="10.0"/>
+        <param name="use_ppm_tolerance" value="false"/>
+        <param name="write_log_messages" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_NoiseFilterGaussian_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="lowmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
+      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="gaussian_width" value="1.0"/>
+        <param name="ppm_tolerance" value="10.0"/>
+        <param name="use_ppm_tolerance" value="false"/>
+        <param name="write_log_messages" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_NoiseFilterGaussian_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="lowmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
+      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="gaussian_width" value="50.0"/>
+        <param name="ppm_tolerance" value="10.0"/>
+        <param name="use_ppm_tolerance" value="false"/>
+        <param name="write_log_messages" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_NoiseFilterGaussian.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterGaussian.html]]></help>
   <expand macro="references"/>
 </tool>