Mercurial > repos > galaxyp > openms_filefilter

diff FileFilter.xml @ 16:86a9dd43dd09 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author: galaxyp
date: Fri, 14 Jun 2024 21:44:21 +0000
parents: fe4e4587d265
--- a/FileFilter.xml	Thu Dec 01 19:19:27 2022 +0000
+++ b/FileFilter.xml	Fri Jun 14 21:44:21 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: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="FileFilter" name="FileFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
+  <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files</description>
   <macros>
     <token name="@EXECUTABLE@">FileFilter</token>
     <import>macros.xml</import>
@@ -15,19 +14,19 @@
 
 ## 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 &&
 #if $spectra.blackorwhitelist.file:
   mkdir spectra.blackorwhitelist.file &&
-  ln -s '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' &&
+  cp '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' &&
 #end if
 #if $consensus.blackorwhitelist.file:
   mkdir consensus.blackorwhitelist.file &&
-  ln -s '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' &&
+  cp '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' &&
 #end if
 #if $id.blacklist:
   mkdir id.blacklist &&
-  ln -s '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' &&
+  cp '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' &&
 #end if
 
 ## Main program call
@@ -63,47 +62,48 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
       <option value="mzML">mzml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-rt" type="text" optional="true" value=":" label="Retention time range to extract" help="">
+    <param argument="-rt" type="text" value=":" label="Retention time range to extract" help="">
       <expand macro="list_string_san" name="rt"/>
     </param>
-    <param argument="-mz" type="text" optional="true" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="">
+    <param argument="-mz" type="text" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="">
       <expand macro="list_string_san" name="mz"/>
     </param>
-    <param argument="-int" type="text" optional="true" value=":" label="Intensity range to extract" help="">
+    <param argument="-int" type="text" value=":" label="Intensity range to extract" help="">
       <expand macro="list_string_san" name="int"/>
     </param>
     <param argument="-sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the output according to RT and m/z" help=""/>
     <section name="peak_options" title="Peak data options" help="" expanded="false">
-      <param name="sn" argument="-peak_options:sn" type="float" optional="true" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help=""/>
+      <param name="sn" argument="-peak_options:sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help=""/>
       <param name="rm_pc_charge" argument="-peak_options:rm_pc_charge" type="text" optional="true" value="" label="Remove MS(2) spectra with these precursor charges" help="All spectra without precursor are kept! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="rm_pc_charge"/>
       </param>
-      <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" optional="true" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
+      <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
         <expand macro="list_string_san" name="pc_mz_range"/>
       </param>
       <param name="pc_mz_list" argument="-peak_options:pc_mz_list" type="text" optional="true" value="" label="List of m/z values" help="If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="pc_mz_list"/>
       </param>
-      <param name="level" argument="-peak_options:level" type="text" optional="true" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="level" argument="-peak_options:level" type="text" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="level"/>
       </param>
       <param name="sort_peaks" argument="-peak_options:sort_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the peaks according to m/z" help=""/>
       <param name="no_chromatograms" argument="-peak_options:no_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No conversion to space-saving real chromatograms" help="e.g. from SRM scans"/>
       <param name="remove_chromatograms" argument="-peak_options:remove_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes chromatograms stored in a file" help=""/>
       <param name="remove_empty" argument="-peak_options:remove_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes spectra and chromatograms without peaks" help=""/>
-      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" optional="true" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
+      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
         <option value="32">32</option>
         <option value="64" selected="true">64</option>
         <expand macro="list_string_san" name="mz_precision"/>
       </param>
-      <param name="int_precision" argument="-peak_options:int_precision" type="select" optional="true" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
+      <param name="int_precision" argument="-peak_options:int_precision" type="select" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
         <option value="32" selected="true">32</option>
         <option value="64">64</option>
         <expand macro="list_string_san" name="int_precision"/>
@@ -111,22 +111,22 @@
       <param name="indexed_file" argument="-peak_options:indexed_file" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to add an index to the file when writing" help=""/>
       <param name="zlib_compression" argument="-peak_options:zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to store data with zlib compression (lossless compression)" help=""/>
       <section name="numpress" title="Numpress compression for peak data" help="" expanded="false">
-        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" optional="true" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
+        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
           <option value="slof">slof</option>
           <expand macro="list_string_san" name="masstime"/>
         </param>
-        <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
-        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" optional="true" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
+        <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
+        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
           <option value="slof">slof</option>
           <expand macro="list_string_san" name="intensity"/>
         </param>
-        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" optional="true" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
+        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
@@ -175,10 +175,10 @@
         <option value="Bruker proprietary method">Bruker proprietary method</option>
         <expand macro="list_string_san" name="remove_activation"/>
       </param>
-      <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" optional="true" value=":" label="Remove MSn scans with a collision energy in the given interval" help="">
+      <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" value=":" label="Remove MSn scans with a collision energy in the given interval" help="">
         <expand macro="list_string_san" name="remove_collision_energy"/>
       </param>
-      <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" optional="true" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="">
+      <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="">
         <expand macro="list_string_san" name="remove_isolation_window_width"/>
       </param>
       <param name="select_zoom" argument="-spectra:select_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Select zoom (enhanced resolution) scans" help=""/>
@@ -220,10 +220,10 @@
         <option value="Bruker proprietary method">Bruker proprietary method</option>
         <expand macro="list_string_san" name="select_activation"/>
       </param>
-      <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" optional="true" value=":" label="Select MSn scans with a collision energy in the given interval" help="">
+      <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" value=":" label="Select MSn scans with a collision energy in the given interval" help="">
         <expand macro="list_string_san" name="select_collision_energy"/>
       </param>
-      <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" optional="true" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="">
+      <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="">
         <expand macro="list_string_san" name="select_isolation_window_width"/>
       </param>
       <param name="select_polarity" argument="-spectra:select_polarity" type="select" optional="true" label="Retain MSn scans with a certain scan polarity" help="">
@@ -232,22 +232,22 @@
         <option value="negative">negative</option>
         <expand macro="list_string_san" name="select_polarity"/>
       </param>
-      <param name="replace_pc_charge" argument="-spectra:replace_pc_charge" type="text" optional="true" value=":" label="Replaces in_charge with out_charge in all precursors" help="">
+      <param name="replace_pc_charge" argument="-spectra:replace_pc_charge" type="text" value=":" label="Replaces in_charge with out_charge in all precursors" help="">
         <expand macro="list_string_san" name="replace_pc_charge"/>
       </param>
       <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by spectral similarity" help="" expanded="false">
         <param name="file" argument="-spectra:blackorwhitelist:file" type="data" format="mzml" optional="true" label="Input file containing MS2 spectra that should be retained or removed from the mzML file" help="Matching tolerances are taken from 'spectra:blackorwhitelist:similarity_threshold|rt|mz' options..  select mzml data sets(s)"/>
-        <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/>
-        <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" optional="true" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/>
-        <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" optional="true" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/>
-        <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" optional="true" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used">
+        <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/>
+        <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/>
+        <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/>
+        <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used">
           <expand macro="list_string_san" name="use_ppm_tolerance"/>
         </param>
         <param name="blacklist" argument="-spectra:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/>
       </section>
     </section>
     <section name="feature" title="Feature data options" help="" expanded="false">
-      <param name="q" argument="-feature:q" type="text" optional="true" value=":" label="Overall quality range to extract [0:1]" help="">
+      <param name="q" argument="-feature:q" type="text" value=":" label="Overall quality range to extract [0:1]" help="">
         <expand macro="list_string_san" name="q"/>
       </param>
     </section>
@@ -262,22 +262,23 @@
         <param name="maps" argument="-consensus:blackorwhitelist:maps" type="text" optional="true" value="" label="Maps used for black/white list filtering" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
           <expand macro="list_integer_valsan" name="maps"/>
         </param>
-        <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" optional="true" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/>
-        <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" optional="true" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/>
+        <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/>
+        <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/>
         <param name="use_ppm_tolerance" argument="-consensus:blackorwhitelist:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If ppm tolerance should be used" help="Otherwise Da are used"/>
       </section>
     </section>
     <section name="f_and_c" title="Feature &amp; Consensus data options" help="" expanded="false">
-      <param name="charge" argument="-f_and_c:charge" type="text" optional="true" value=":" label="Charge range to extract" help="">
+      <param name="charge" argument="-f_and_c:charge" type="text" value=":" label="Charge range to extract" help="">
         <expand macro="list_string_san" name="charge"/>
       </param>
-      <param name="size" argument="-f_and_c:size" type="text" optional="true" value=":" label="Size range to extract" help="">
+      <param name="size" argument="-f_and_c:size" type="text" value=":" label="Size range to extract" help="">
         <expand macro="list_string_san" name="size"/>
       </param>
       <param name="remove_meta" argument="-f_and_c:remove_meta" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="remove_meta"/>
         <expand macro="list_string_san" name="remove_meta"/>
       </param>
+      <param name="remove_hull" argument="-f_and_c:remove_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove hull from features" help=""/>
     </section>
     <section name="id" title="ID options" help="The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -&gt; remove_clashes -&gt; keep_best_score_id -&gt; sequences_whitelist  / accessions_whitelist" expanded="false">
       <param name="remove_clashes" argument="-id:remove_clashes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with id clashes (different sequences mapped to one feature)" help=""/>
@@ -286,7 +287,7 @@
         <expand macro="list_string_val" name="sequences_whitelist"/>
         <expand macro="list_string_san" name="sequences_whitelist"/>
       </param>
-      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" optional="true" label="Comparison method used to determine if a feature is whitelisted" help="">
+      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" label="Comparison method used to determine if a feature is whitelisted" help="">
         <option value="substring" selected="true">substring</option>
         <option value="exact">exact</option>
         <expand macro="list_string_san" name="sequence_comparison_method"/>
@@ -299,26 +300,26 @@
       <param name="remove_unannotated_features" argument="-id:remove_unannotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features without annotations" help=""/>
       <param name="remove_unassigned_ids" argument="-id:remove_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassigned peptide identifications" help=""/>
       <param name="blacklist" argument="-id:blacklist" type="data" format="idxml" optional="true" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file" help="Matching tolerances are taken from 'id:rt' and 'id:mz' options.. This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches select idxml data sets(s)"/>
-      <param name="rt" argument="-id:rt" type="float" optional="true" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/>
-      <param name="mz" argument="-id:mz" type="float" optional="true" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/>
+      <param name="rt" argument="-id:rt" type="float" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/>
+      <param name="mz" argument="-id:mz" type="float" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/>
       <param name="blacklist_imperfect" argument="-id:blacklist_imperfect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow for mismatching precursor positions (see 'id:blacklist')" help=""/>
     </section>
     <section name="algorithm" title="S/N algorithm section" help="" expanded="false">
       <section name="SignalToNoise" title="" help="" expanded="false">
-        <param name="max_intensity" argument="-algorithm:SignalToNoise: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 be added to the LAST histogram bin. 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). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
-        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise: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:SignalToNoise: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:SignalToNoise: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:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-        <param name="min_required_elements" argument="-algorithm:SignalToNoise: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:SignalToNoise: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:SignalToNoise: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 be added to the LAST histogram bin. 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). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
+        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise: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:SignalToNoise: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:SignalToNoise: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:SignalToNoise:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+        <param name="min_required_elements" argument="-algorithm:SignalToNoise: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:SignalToNoise:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
         <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <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>
@@ -337,14 +338,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileFilter_1 -->
+  <tests>
+    <!-- TOPP_FileFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":30"/>
       <param name="mz" value=":1000"/>
@@ -352,9 +354,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -373,16 +373,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -396,11 +391,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -409,14 +402,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -443,6 +434,9 @@
           <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_FileFilter_2 -->
     <test expect_num_outputs="2">
@@ -451,7 +445,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value="30:"/>
       <param name="mz" value="1000:"/>
@@ -459,9 +453,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -480,16 +472,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -503,11 +490,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -516,14 +501,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -550,6 +533,9 @@
           <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_FileFilter_3 -->
     <test expect_num_outputs="2">
@@ -558,7 +544,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -566,9 +552,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -587,16 +571,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -610,11 +589,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -623,14 +600,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -657,6 +632,9 @@
           <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_FileFilter_4 -->
     <test expect_num_outputs="2">
@@ -665,7 +643,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_4_input.mzML"/>
-      <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -673,9 +651,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -694,16 +670,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="true"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -717,11 +688,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -730,14 +699,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -764,6 +731,9 @@
           <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_FileFilter_5 -->
     <test expect_num_outputs="2">
@@ -772,7 +742,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_5_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":1000"/>
       <param name="mz" value=":480"/>
@@ -780,9 +750,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -801,16 +769,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -824,11 +787,9 @@
         <param name="q" value=":0.6"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -837,14 +798,12 @@
       <section name="f_and_c">
         <param name="charge" value=":3"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -871,6 +830,9 @@
           <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_FileFilter_6 -->
     <test expect_num_outputs="2">
@@ -879,7 +841,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_6_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="1000:"/>
       <param name="mz" value="440:"/>
@@ -887,9 +849,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -908,16 +868,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -931,11 +886,9 @@
         <param name="q" value="0.51:"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -944,14 +897,12 @@
       <section name="f_and_c">
         <param name="charge" value="3:"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -978,6 +929,9 @@
           <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_FileFilter_7 -->
     <test expect_num_outputs="2">
@@ -986,7 +940,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_7_input.mzML"/>
-      <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_7_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -994,9 +948,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1015,16 +967,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1038,11 +985,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1051,14 +996,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1085,6 +1028,9 @@
           <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_FileFilter_8 -->
     <test expect_num_outputs="2">
@@ -1093,7 +1039,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_8_input.consensusXML"/>
-      <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value="600:1400"/>
       <param name="mz" value="700:2300"/>
@@ -1101,9 +1047,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1122,16 +1066,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1145,11 +1084,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1158,14 +1095,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1192,6 +1127,9 @@
           <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_FileFilter_9 -->
     <test expect_num_outputs="2">
@@ -1200,7 +1138,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_9_input.mzML"/>
-      <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_9_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1208,9 +1146,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1230,15 +1166,11 @@
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
         <param name="remove_mode" value="SelectedIonMonitoring"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1252,11 +1184,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1265,14 +1195,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1299,6 +1227,9 @@
           <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_FileFilter_10 -->
     <test expect_num_outputs="2">
@@ -1307,7 +1238,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_10_input.mzML"/>
-      <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1315,9 +1246,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1336,16 +1265,12 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
         <param name="remove_activation" value="Collision-induced dissociation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1359,11 +1284,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1372,14 +1295,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1406,6 +1327,9 @@
           <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_FileFilter_11 -->
     <test expect_num_outputs="2">
@@ -1414,7 +1338,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_11_input.mzML"/>
-      <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_11_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1422,9 +1346,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1443,16 +1365,12 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
         <param name="remove_activation" value="Plasma desorption"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1466,11 +1384,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1479,14 +1395,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1513,6 +1427,9 @@
           <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_FileFilter_12 -->
     <test expect_num_outputs="2">
@@ -1521,7 +1438,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_12_input.mzML"/>
-      <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_12_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1529,9 +1446,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1550,16 +1465,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1573,11 +1483,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1586,14 +1494,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1620,6 +1526,9 @@
           <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_FileFilter_13 -->
     <test expect_num_outputs="2">
@@ -1628,7 +1537,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_13_input.consensusXML"/>
-      <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1636,9 +1545,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1657,16 +1564,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1684,7 +1586,6 @@
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1693,14 +1594,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1727,6 +1626,9 @@
           <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_FileFilter_14 -->
     <test expect_num_outputs="2">
@@ -1735,7 +1637,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_14_input.consensusXML"/>
-      <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1743,9 +1645,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1764,16 +1664,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1791,7 +1686,6 @@
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1800,14 +1694,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1834,6 +1726,9 @@
           <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_FileFilter_15 -->
     <test expect_num_outputs="2">
@@ -1842,7 +1737,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1850,9 +1745,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1871,16 +1764,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1894,11 +1782,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1907,14 +1793,13 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -1941,6 +1826,9 @@
           <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_FileFilter_16 -->
     <test expect_num_outputs="2">
@@ -1949,7 +1837,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -1957,9 +1845,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1978,16 +1864,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2001,11 +1882,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2014,14 +1893,13 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2048,6 +1926,9 @@
           <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_FileFilter_17 -->
     <test expect_num_outputs="2">
@@ -2056,7 +1937,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -2064,9 +1945,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2085,16 +1964,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2108,11 +1982,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2121,14 +1993,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="true"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2155,6 +2025,9 @@
           <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_FileFilter_18 -->
     <test expect_num_outputs="2">
@@ -2163,7 +2036,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_18_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2171,9 +2044,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2192,16 +2063,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2215,11 +2081,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2228,14 +2092,13 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2262,6 +2125,9 @@
           <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_FileFilter_19 -->
     <test expect_num_outputs="2">
@@ -2270,7 +2136,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_19_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -2278,9 +2144,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2299,16 +2163,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2322,11 +2181,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2335,14 +2192,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="true"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2369,6 +2224,9 @@
           <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_FileFilter_20 -->
     <test expect_num_outputs="2">
@@ -2377,7 +2235,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2385,9 +2243,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2406,16 +2262,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2429,11 +2280,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2442,12 +2291,11 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
         <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
         <param name="remove_annotated_features" value="false"/>
@@ -2476,6 +2324,9 @@
           <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_FileFilter_21 -->
     <test expect_num_outputs="2">
@@ -2484,7 +2335,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2492,9 +2343,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2513,16 +2362,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2536,11 +2380,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2549,14 +2391,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="true"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="true"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2583,6 +2423,9 @@
           <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_FileFilter_22 -->
     <test expect_num_outputs="2">
@@ -2591,7 +2434,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2599,9 +2442,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2620,16 +2461,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2643,11 +2479,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2657,13 +2491,12 @@
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2690,6 +2523,9 @@
           <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_FileFilter_23 -->
     <test expect_num_outputs="2">
@@ -2698,7 +2534,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2706,9 +2542,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2727,16 +2561,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2750,11 +2579,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2764,13 +2591,12 @@
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2797,6 +2623,9 @@
           <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_FileFilter_24 -->
     <test expect_num_outputs="2">
@@ -2805,7 +2634,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2813,9 +2642,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2834,16 +2661,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2857,11 +2679,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2871,13 +2691,12 @@
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2904,6 +2723,9 @@
           <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_FileFilter_25 -->
     <test expect_num_outputs="2">
@@ -2912,7 +2734,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2920,9 +2742,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2941,16 +2761,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2964,11 +2779,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2977,14 +2790,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3012,6 +2823,9 @@
           <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_FileFilter_26 -->
     <test expect_num_outputs="2">
@@ -3020,7 +2834,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3028,9 +2842,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3049,16 +2861,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3072,11 +2879,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3085,14 +2890,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3120,6 +2923,9 @@
           <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_FileFilter_28 -->
     <test expect_num_outputs="2">
@@ -3128,7 +2934,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3136,9 +2942,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3157,16 +2961,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3180,11 +2979,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3193,14 +2990,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3227,6 +3022,9 @@
           <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_FileFilter_29 -->
     <test expect_num_outputs="2">
@@ -3235,7 +3033,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3243,9 +3041,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3264,16 +3060,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3287,11 +3078,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3300,14 +3089,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3334,6 +3121,9 @@
           <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_FileFilter_30 -->
     <test expect_num_outputs="2">
@@ -3342,7 +3132,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3350,9 +3140,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3371,16 +3159,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3394,11 +3177,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3407,14 +3188,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3441,6 +3220,9 @@
           <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_FileFilter_31 -->
     <test expect_num_outputs="2">
@@ -3449,7 +3231,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3457,9 +3239,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3478,16 +3258,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":2"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3501,11 +3276,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3514,14 +3287,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3548,6 +3319,9 @@
           <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_FileFilter_32 -->
     <test expect_num_outputs="2">
@@ -3556,7 +3330,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3564,9 +3338,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3585,16 +3357,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":2"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3608,11 +3375,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3621,14 +3386,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3655,6 +3418,9 @@
           <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_FileFilter_33 -->
     <test expect_num_outputs="2">
@@ -3663,7 +3429,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3671,9 +3437,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3692,16 +3456,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":35"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3715,11 +3474,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3728,14 +3485,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3762,6 +3517,9 @@
           <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_FileFilter_34 -->
     <test expect_num_outputs="2">
@@ -3770,7 +3528,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3778,9 +3536,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3799,16 +3555,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":35"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3822,11 +3573,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3835,14 +3584,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3869,6 +3616,9 @@
           <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_FileFilter_35 -->
     <test expect_num_outputs="2">
@@ -3877,7 +3627,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_35_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3885,9 +3635,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3906,16 +3654,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3929,11 +3672,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3942,14 +3683,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3976,6 +3715,9 @@
           <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_FileFilter_36 -->
     <test expect_num_outputs="2">
@@ -3984,7 +3726,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_36_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3992,9 +3734,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4013,16 +3753,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4036,11 +3771,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4049,14 +3782,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4083,6 +3814,9 @@
           <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_FileFilter_37 -->
     <test expect_num_outputs="2">
@@ -4091,7 +3825,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_37_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4099,9 +3833,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4120,16 +3852,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4143,11 +3870,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4156,14 +3881,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4190,6 +3913,9 @@
           <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_FileFilter_38 -->
     <test expect_num_outputs="2">
@@ -4198,7 +3924,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_38_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4206,9 +3932,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4227,16 +3951,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4250,11 +3969,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4263,14 +3980,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4297,6 +4012,9 @@
           <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_FileFilter_40 -->
     <test expect_num_outputs="2">
@@ -4305,7 +4023,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_40_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4313,9 +4031,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4334,13 +4050,9 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
         <param name="select_polarity" value="positive"/>
@@ -4357,11 +4069,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4370,14 +4080,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4404,6 +4112,9 @@
           <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_FileFilter_41 -->
     <test expect_num_outputs="2">
@@ -4412,7 +4123,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_41_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4420,9 +4131,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4441,13 +4150,9 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
         <param name="select_polarity" value="negative"/>
@@ -4464,11 +4169,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4477,14 +4180,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4511,6 +4212,9 @@
           <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_FileFilter_42 -->
     <test expect_num_outputs="2">
@@ -4519,7 +4223,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_42_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4527,9 +4231,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4548,16 +4250,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4571,11 +4268,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4584,14 +4279,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4618,6 +4311,9 @@
           <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_FileFilter_43 -->
     <test expect_num_outputs="2">
@@ -4626,7 +4322,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_43_input.mzML"/>
-      <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_43_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4634,9 +4330,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4655,16 +4349,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4678,11 +4367,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4691,14 +4378,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4725,6 +4410,9 @@
           <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_FileFilter_43_read_again -->
     <test expect_num_outputs="2">
@@ -4732,8 +4420,8 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
-      <param name="in" value="FileFilter_43.tmp.mzML"/>
-      <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta_frac="0.7"/>
+      <param name="in" value="FileFilter_43_output.mzML"/>
+      <output name="out" value="FileFilter_43.dummy.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4741,9 +4429,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4762,16 +4448,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4785,11 +4466,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4798,14 +4477,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4832,6 +4509,9 @@
           <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_FileFilter_44 -->
     <test expect_num_outputs="2">
@@ -4840,7 +4520,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_44_input.mzML"/>
-      <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_44_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4848,9 +4528,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4869,16 +4547,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4892,11 +4565,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4905,14 +4576,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4939,6 +4608,9 @@
           <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_FileFilter_45 -->
     <test expect_num_outputs="2">
@@ -4947,7 +4619,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_45_input.featureXML"/>
-      <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_45_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4955,9 +4627,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4976,16 +4646,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4999,11 +4664,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5012,14 +4675,13 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5046,6 +4708,9 @@
           <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_FileFilter_46 -->
     <test expect_num_outputs="2">
@@ -5054,7 +4719,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_46_input.featureXML"/>
-      <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_46_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5062,9 +4727,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5083,16 +4746,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -5106,11 +4764,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5119,14 +4775,13 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
         <param name="sequence_comparison_method" value="exact"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5153,6 +4808,9 @@
           <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_FileFilter_47 -->
     <test expect_num_outputs="2">
@@ -5161,7 +4819,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_47_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5169,9 +4827,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5190,16 +4846,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="file" value="FileFilter_47_input_select.mzML"/>
@@ -5214,11 +4865,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5227,14 +4876,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5261,6 +4908,9 @@
           <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_FileFilter_48 -->
     <test expect_num_outputs="2">
@@ -5269,7 +4919,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_48_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5277,9 +4927,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5298,16 +4946,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="file" value="FileFilter_47_input_select.mzML"/>
@@ -5322,11 +4965,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5335,14 +4976,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5369,6 +5008,9 @@
           <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_FileFilter_49 -->
     <test expect_num_outputs="2">
@@ -5377,7 +5019,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_49_input.mzML"/>
-      <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_49_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5385,9 +5027,7 @@
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5406,16 +5046,11 @@
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -5429,11 +5064,9 @@
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5442,14 +5075,12 @@
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5476,11 +5107,14 @@
           <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[Extracts or manipulates portions of data from peak, feature or consensus-feature files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileFilter.html]]></help>
   <expand macro="references"/>
 </tool>
author	galaxyp
date	Fri, 14 Jun 2024 21:44:21 +0000
parents	fe4e4587d265
children