--- a/SpectraFilterNormalizer.xml	Thu Dec 01 19:10:52 2022 +0000
+++ b/SpectraFilterNormalizer.xml	Fri Jun 14 21:30:31 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: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Normalizes intensity of peak spectra.</description>
+  <description>Normalizes intensity of peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterNormalizer</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
@@ -39,9 +38,9 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="method" argument="-algorithm:method" type="select" optional="true" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
+      <param name="method" argument="-algorithm:method" type="select" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
         <option value="to_one" selected="true">to_one</option>
         <option value="to_TIC">to_TIC</option>
         <expand macro="list_string_san" name="method"/>
@@ -49,7 +48,7 @@
     </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>
@@ -63,15 +62,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Normalizes intensity of peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>