--- a/FeatureLinkerUnlabeledQT.xml	Thu Dec 01 19:06:27 2022 +0000
+++ b/FeatureLinkerUnlabeledQT.xml	Fri Jun 14 21:36:52 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: [Map Alignment]-->
+<!--Proposed Tool Section: [Feature Linking]-->
 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding features from multiple maps.</description>
+  <description>Groups corresponding features from multiple maps</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #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
 
 ## Main program call
@@ -62,41 +61,41 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/>
-      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
-      <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" optional="true" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
-      <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" optional="true" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
-      <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
+      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
+      <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
+      <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
+      <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
       <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
       <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
       <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
-        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
+        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="unit"/>
         </param>
-        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
+        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
@@ -105,7 +104,7 @@
     </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>
@@ -119,7 +118,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -128,7 +128,7 @@
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -161,6 +161,9 @@
           <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_FeatureLinkerUnlabeledQT_2 -->
     <test expect_num_outputs="2">
@@ -169,9 +172,9 @@
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledQT_1_output_0.consensusXML,FeatureLinkerUnlabeledQT_1_output_1.consensusXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="true"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -204,6 +207,9 @@
           <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_FeatureLinkerUnlabeledQT_3 -->
     <test expect_num_outputs="2">
@@ -214,7 +220,7 @@
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -247,6 +253,9 @@
           <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_FeatureLinkerUnlabeledQT_4 -->
     <test expect_num_outputs="2">
@@ -257,7 +266,7 @@
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="true"/>
@@ -290,6 +299,9 @@
           <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_FeatureLinkerUnlabeledQT_5 -->
     <test expect_num_outputs="2">
@@ -300,7 +312,7 @@
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -333,6 +345,9 @@
           <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_FeatureLinkerUnlabeledQT_6 -->
     <test expect_num_outputs="2">
@@ -343,7 +358,7 @@
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="true"/>
@@ -376,11 +391,14 @@
           <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[Groups corresponding features from multiple maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
   <expand macro="references"/>
 </tool>