--- a/ProteinQuantifier.xml	Thu Dec 01 19:18:55 2022 +0000
+++ b/ProteinQuantifier.xml	Fri Jun 14 21:34:51 2024 +0000
@@ -1,4 +1,3 @@
-<?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: [Quantitation]-->
 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,14 +14,14 @@
 
 ## 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)' &&
 #if $protein_groups:
   mkdir protein_groups &&
-  ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
+  cp '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
 #end if
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -84,43 +83,50 @@
     <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,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
-    <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+    <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. via the ProteinInference tool).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
-    <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
-    <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help="">
-      <option value="median" selected="true">median</option>
-      <option value="mean">mean</option>
-      <option value="weighted_mean">weighted_mean</option>
-      <option value="sum">sum</option>
-      <expand macro="list_string_san" name="average"/>
+    <param argument="-method" type="select" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!">
+      <option value="top" selected="true">top</option>
+      <option value="iBAQ">iBAQ</option>
+      <expand macro="list_string_san" name="method"/>
     </param>
-    <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
     <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
     <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
     <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
     <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
+    <section name="top" title="Additional options for custom quantification using top N peptides" help="" expanded="false">
+      <param name="N" argument="-top:N" type="integer" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
+      <param name="aggregate" argument="-top:aggregate" type="select" label="Aggregation method used to compute protein abundances from peptide abundances" help="">
+        <option value="median" selected="true">median</option>
+        <option value="mean">mean</option>
+        <option value="weighted_mean">weighted_mean</option>
+        <option value="sum">sum</option>
+        <expand macro="list_string_san" name="aggregate"/>
+      </param>
+      <param name="include_all" argument="-top:include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)" help=""/>
+    </section>
     <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
       <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
-      <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
+      <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'N 0',all peptides that occur in every sample are considered.. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
     </section>
     <section name="format" title="Output formatting options" help="" expanded="false">
       <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
         <expand macro="list_string_san" name="separator"/>
       </param>
-      <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+      <param name="quoting" argument="-format:quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
         <option value="none">none</option>
         <option value="double" selected="true">double</option>
         <option value="escape">escape</option>
         <expand macro="list_string_san" name="quoting"/>
       </param>
-      <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
+      <param name="replacement" argument="-format:replacement" type="text" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
         <expand macro="list_string_san" name="replacement"/>
       </param>
     </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>
@@ -148,22 +154,26 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinQuantifier_1 -->
+  <tests>
+    <!-- TOPP_ProteinQuantifier_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="median"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -179,6 +189,9 @@
           <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_ProteinQuantifier_2 -->
     <test expect_num_outputs="3">
@@ -187,15 +200,18 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="true"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="2"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -211,6 +227,9 @@
           <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_ProteinQuantifier_3 -->
     <test expect_num_outputs="3">
@@ -219,15 +238,18 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="mean"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="2"/>
+        <param name="aggregate" value="mean"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -243,6 +265,9 @@
           <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_ProteinQuantifier_4 -->
     <test expect_num_outputs="2">
@@ -251,14 +276,17 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -274,6 +302,9 @@
           <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_ProteinQuantifier_5 -->
     <test expect_num_outputs="2">
@@ -282,14 +313,17 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -305,6 +339,9 @@
           <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_ProteinQuantifier_6 -->
     <test expect_num_outputs="2">
@@ -313,14 +350,17 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -336,6 +376,9 @@
           <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_ProteinQuantifier_7 -->
     <test expect_num_outputs="2">
@@ -344,14 +387,17 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -367,6 +413,9 @@
           <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_ProteinQuantifier_8 -->
     <test expect_num_outputs="2">
@@ -375,14 +424,17 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -398,6 +450,9 @@
           <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_ProteinQuantifier_9 -->
     <test expect_num_outputs="3">
@@ -406,15 +461,18 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="mztab" value="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -430,6 +488,9 @@
           <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_ProteinQuantifier_12 -->
     <test expect_num_outputs="2">
@@ -438,14 +499,54 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="true"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
+      <section name="consensus">
+        <param name="normalize" value="false"/>
+        <param name="fix_peptides" value="true"/>
+      </section>
+      <section name="format">
+        <param name="separator" value=""/>
+        <param name="quoting" value="double"/>
+        <param name="replacement" value="_"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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_ProteinQuantifier_13 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
+      <output name="out" value="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
+      <param name="best_charge_and_fraction" value="false"/>
+      <param name="greedy_group_resolution" value="false"/>
+      <param name="ratios" value="false"/>
+      <param name="ratiosSILAC" value="true"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -461,37 +562,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test>
-    <!-- TOPP_ProteinQuantifier_13 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="true"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <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_ProteinQuantifier_14 -->
     <test expect_num_outputs="3">
@@ -500,15 +573,18 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.idXML"/>
-      <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -524,11 +600,89 @@
           <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_ProteinQuantifier_15 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
+      <output name="out" value="ProteinQuantifier_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="iBAQ"/>
+      <param name="best_charge_and_fraction" value="false"/>
+      <param name="greedy_group_resolution" value="false"/>
+      <param name="ratios" value="false"/>
+      <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="false"/>
+      </section>
+      <section name="consensus">
+        <param name="normalize" value="false"/>
+        <param name="fix_peptides" value="false"/>
+      </section>
+      <section name="format">
+        <param name="separator" value=""/>
+        <param name="quoting" value="double"/>
+        <param name="replacement" value="_"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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_ProteinQuantifier_16 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ProteinQuantifier_16_input.consensusXML"/>
+      <param name="design" value="ProteinQuantifier_16_input.tsv" ftype="tabular"/>
+      <output name="out" value="ProteinQuantifier_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
+      <param name="best_charge_and_fraction" value="false"/>
+      <param name="greedy_group_resolution" value="false"/>
+      <param name="ratios" value="false"/>
+      <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="true"/>
+      </section>
+      <section name="consensus">
+        <param name="normalize" value="false"/>
+        <param name="fix_peptides" value="false"/>
+      </section>
+      <section name="format">
+        <param name="separator" value=""/>
+        <param name="quoting" value="double"/>
+        <param name="replacement" value="_"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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[Compute peptide and protein abundances
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinQuantifier.html]]></help>
   <expand macro="references"/>
 </tool>