--- a/MapRTTransformer.xml	Thu Dec 01 19:14:37 2022 +0000
+++ b/MapRTTransformer.xml	Fri Jun 14 21:46:00 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]-->
 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies retention time transformations to maps.</description>
+  <description>Applies retention time transformations to maps</description>
   <macros>
     <token name="@EXECUTABLE@">MapRTTransformer</token>
     <import>macros.xml</import>
@@ -16,13 +15,13 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
 mkdir trafo_in &&
-ln -s '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
+cp '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
 #end if
@@ -67,11 +66,11 @@
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="true" label="Input file to transform (separated by blanks)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
-    <param argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
+    <param argument="-trafo_in" type="data" format="trafoxml" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
     <param argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/>
     <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output file" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="none" selected="true">none</option>
         <option value="linear">linear</option>
         <option value="b_spline">b_spline</option>
@@ -81,48 +80,48 @@
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
-          <option value=""></option>
+          <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
-          <option value=""></option>
+          <option value="y" selected="true">y</option>
           <expand macro="list_string_san" name="y_weight"/>
         </param>
-        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
-        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
-        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
-        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
+        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
+        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
+        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
       </section>
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
-        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
           <option value="global_linear">global_linear</option>
           <expand macro="list_string_san" name="extrapolate"/>
         </param>
-        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
       </section>
       <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
-        <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-        <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="span" argument="-model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -130,13 +129,13 @@
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -146,7 +145,7 @@
     </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>
@@ -170,14 +169,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapRTTransformer_1 -->
+  <tests>
+    <!-- TOPP_MapRTTransformer_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="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -185,8 +185,8 @@
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -216,6 +216,9 @@
           <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_MapRTTransformer_2 -->
     <test expect_num_outputs="2">
@@ -224,7 +227,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_2_input.mzML"/>
-      <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -232,8 +235,8 @@
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -263,6 +266,9 @@
           <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_MapRTTransformer_3 -->
     <test expect_num_outputs="2">
@@ -271,15 +277,15 @@
         <param name="test" value="true"/>
       </section>
       <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
-      <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
+      <output name="trafo_out" value="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
       <param name="invert" value="true"/>
       <param name="store_original_rt" value="false"/>
       <section name="model">
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -309,6 +315,9 @@
           <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_MapRTTransformer_4 -->
     <test expect_num_outputs="2">
@@ -317,7 +326,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
-      <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -325,8 +334,8 @@
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -356,6 +365,9 @@
           <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_MapRTTransformer_5 -->
     <test expect_num_outputs="2">
@@ -364,7 +376,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -372,8 +384,8 @@
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -403,6 +415,9 @@
           <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_MapRTTransformer_6 -->
     <test expect_num_outputs="2">
@@ -411,7 +426,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="true"/>
@@ -419,8 +434,8 @@
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -450,11 +465,14 @@
           <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[Applies retention time transformations to maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapRTTransformer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapRTTransformer.html]]></help>
   <expand macro="references"/>
 </tool>