--- a/FuzzyDiff.xml	Thu Dec 01 19:04:01 2022 +0000
+++ b/FuzzyDiff.xml	Fri Jun 14 21:28:23 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: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Compares two files, tolerating numeric differences.</description>
+  <description>Compares two files, tolerating numeric differences</description>
   <macros>
     <token name="@EXECUTABLE@">FuzzyDiff</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in1 &&
-ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
+cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
 mkdir in2 &&
-ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
+cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
 
 ## Main program call
 
@@ -40,15 +39,15 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
-    <param argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
-    <param argument="-ratio" type="float" optional="true" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied.  Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
-    <param argument="-absdiff" type="float" optional="true" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
-    <param argument="-verbose" type="integer" optional="true" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/>
-    <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
-    <param argument="-first_column" type="integer" optional="true" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
+    <param argument="-in1" type="data" format="txt" label="first input file" help=" select txt data sets(s)"/>
+    <param argument="-in2" type="data" format="txt" label="second input file" help=" select txt data sets(s)"/>
+    <param argument="-ratio" type="float" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied.  Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
+    <param argument="-absdiff" type="float" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
+    <param argument="-verbose" type="integer" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/>
+    <param argument="-tab_width" type="integer" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
+    <param argument="-first_column" type="integer" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-whitelist" type="text" optional="true" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param argument="-whitelist" type="text" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="whitelist"/>
         <expand macro="list_string_san" name="whitelist"/>
       </param>
@@ -57,7 +56,7 @@
         <expand macro="list_string_san" name="matched_whitelist"/>
       </param>
       <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>
@@ -73,11 +72,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_FuzzyDiff_3 -->
+  <tests>
+    <!-- TOPP_FuzzyDiff_3 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
-        <param name="matched_whitelist" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -94,11 +93,14 @@
           <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[Compares two files, tolerating numeric differences.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FuzzyDiff.html]]></help>
   <expand macro="references"/>
 </tool>