--- a/FeatureLinkerLabeled.xml	Thu Dec 01 19:09:37 2022 +0000
+++ b/FeatureLinkerLabeled.xml	Fri Jun 14 21:30:23 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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding isotope-labeled features in a feature map.</description>
+  <description>Groups corresponding isotope-labeled features in a feature map</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,21 +38,21 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" label="Input file" help=" select featurexml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
-      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
-      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
-      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
-      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
+      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
+      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
+      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="mz_pair_dists"/>
       </param>
-      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
+      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
       <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
     </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>
@@ -67,14 +66,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerLabeled_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerLabeled_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="FeatureLinkerLabeled_1_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="rt_estimate" value="false"/>
         <param name="rt_pair_dist" value="-1.0"/>
@@ -90,6 +90,9 @@
           <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_FeatureLinkerLabeled_2 -->
     <test expect_num_outputs="2">
@@ -98,7 +101,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="rt_estimate" value="true"/>
         <param name="rt_pair_dist" value="-121.0382"/>
@@ -114,11 +117,14 @@
           <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 isotope-labeled features in a feature map.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
   <expand macro="references"/>
 </tool>