--- a/PeakPickerWavelet.xml	Thu Dec 01 19:16:26 2022 +0000
+++ b/PeakPickerWavelet.xml	Fri Jun 14 21:37:22 2024 +0000
@@ -1,8 +1,7 @@
-<?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]-->
+<!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <description>Finds mass spectrometric peaks in profile mass spectra</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerWavelet</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,72 +38,72 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input profile data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
-      <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
-      <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
+      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
+      <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
+      <param name="peak_width" argument="-algorithm:peak_width" type="float" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
       <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/>
-      <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" optional="true" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
-      <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" optional="true" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
+      <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
+      <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
       <section name="optimization" title="" help="" expanded="false">
-        <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
+        <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
         <section name="penalties" title="" help="" expanded="false">
-          <param name="position" argument="-algorithm:optimization:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
-          <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
-          <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
-          <param name="height" argument="-algorithm:optimization:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
+          <param name="position" argument="-algorithm:optimization:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
+          <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
+          <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
+          <param name="height" argument="-algorithm:optimization:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
         </section>
         <section name="2d" title="" help="" expanded="false">
-          <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
-          <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
+          <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
+          <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
         </section>
       </section>
       <section name="thresholds" title="" help="" expanded="false">
-        <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
-        <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
-        <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
-        <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
-        <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" optional="true" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
+        <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
+        <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
+        <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
+        <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
+        <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
       </section>
       <section name="wavelet_transform" title="" help="" expanded="false">
-        <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" optional="true" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
+        <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
       </section>
       <section name="deconvolution" title="" help="" expanded="false">
         <param name="deconvolution" argument="-algorithm:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help=""/>
-        <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" optional="true" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-        <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" optional="true" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
-        <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" optional="true" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
-        <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" optional="true" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
+        <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+        <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
+        <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
+        <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
         <section name="fitting" title="" help="" expanded="false">
-          <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" optional="true" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-          <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
-          <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
-          <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
+          <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+          <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
+          <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
+          <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
           <section name="penalties" title="" help="" expanded="false">
-            <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
-            <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
-            <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
-            <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
+            <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
+            <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
+            <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
+            <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
           </section>
         </section>
       </section>
       <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
-        <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
-        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
-        <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
-        <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
-        <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-        <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-        <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
-        <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
-        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
+        <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
+        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
+        <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
+        <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
+        <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+        <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+        <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
+        <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
+        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/>
       <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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -118,7 +117,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PeakPickerWavelet_1 -->
+  <tests>
+    <!-- TOPP_PeakPickerWavelet_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="write_peak_meta_data" value="true"/>
@@ -126,7 +126,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -194,6 +194,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_2 -->
     <test expect_num_outputs="2">
@@ -203,7 +206,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="2.0"/>
         <param name="centroid_percentage" value="0.8"/>
@@ -271,6 +274,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_4 -->
     <test expect_num_outputs="2">
@@ -280,7 +286,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -348,6 +354,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_5 -->
     <test expect_num_outputs="2">
@@ -357,7 +366,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -425,11 +434,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerWavelet.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerWavelet.html]]></help>
   <expand macro="references"/>
 </tool>