--- a/FeatureFinderIsotopeWavelet.xml	Thu Dec 01 19:04:44 2022 +0000
+++ b/FeatureFinderIsotopeWavelet.xml	Fri Jun 14 21:36:37 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: [Quantitation]-->
 <tool id="FeatureFinderIsotopeWavelet" name="FeatureFinderIsotopeWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects two-dimensional features in LC-MS data.</description>
+  <description>Detects two-dimensional features in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderIsotopeWavelet</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
@@ -39,11 +38,11 @@
     <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 section" help="" expanded="false">
-      <param name="max_charge" argument="-algorithm:max_charge" type="integer" optional="true" min="1" value="3" label="The maximal charge state to be considered" help=""/>
-      <param name="intensity_threshold" argument="-algorithm:intensity_threshold" type="float" optional="true" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="If you set intensity_threshold=-1, t' will be zero.. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
-      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" optional="true" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
+      <param name="max_charge" argument="-algorithm:max_charge" type="integer" min="1" value="3" label="The maximal charge state to be considered" help=""/>
+      <param name="intensity_threshold" argument="-algorithm:intensity_threshold" type="float" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="If you set intensity_threshold=-1, t' will be zero.. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
+      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
         <option value="ref" selected="true">ref</option>
         <option value="trans">trans</option>
         <option value="corrected">corrected</option>
@@ -52,13 +51,13 @@
       <param name="check_ppm" argument="-algorithm:check_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enables/disables a ppm test vs" help="the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied"/>
       <param name="hr_data" argument="-algorithm:hr_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Must be true in case of high-resolution data" help="i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure"/>
       <section name="sweep_line" title="" help="" expanded="false">
-        <param name="rt_votes_cutoff" argument="-algorithm:sweep_line:rt_votes_cutoff" type="integer" optional="true" min="0" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" help=""/>
-        <param name="rt_interleave" argument="-algorithm:sweep_line:rt_interleave" type="integer" optional="true" min="0" value="1" label="Defines the maximum number of scans (w.r.t" help="rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value"/>
+        <param name="rt_votes_cutoff" argument="-algorithm:sweep_line:rt_votes_cutoff" type="integer" min="0" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" help=""/>
+        <param name="rt_interleave" argument="-algorithm:sweep_line:rt_interleave" type="integer" min="0" value="1" label="Defines the maximum number of scans (w.r.t" help="rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value"/>
       </section>
     </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>
@@ -72,15 +71,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-    <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--just use the input of another FeatureFinder -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
+      <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIsotopeWavelet.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIsotopeWavelet.html]]></help>
   <expand macro="references"/>
 </tool>