--- a/InternalCalibration.xml	Thu Dec 01 19:14:27 2022 +0000
+++ b/InternalCalibration.xml	Fri Jun 14 21:27:54 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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies an internal mass recalibration.</description>
+  <description>Applies an internal mass recalibration</description>
   <macros>
     <token name="@EXECUTABLE@">InternalCalibration</token>
     <import>macros.xml</import>
@@ -15,15 +14,15 @@
 
 ## 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 &&
 #if $cal.id_in:
   mkdir cal.id_in &&
-  ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
+  cp '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
 #end if
 #if $cal.lock_in:
   mkdir cal.lock_in &&
-  ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
+  cp '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
 #end if
 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir cal_lock_out &&
@@ -118,18 +117,18 @@
     <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
-    <param argument="-ppm_match_tolerance" type="float" optional="true" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
-    <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
+    <param argument="-ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
+    <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="ms_level"/>
     </param>
-    <param argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
+    <param argument="-RT_chunking" type="float" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
     <section name="cal" title="Chose one of two optional input files ('id_in' or 'lock_in') to define the calibration masses/function" help="" expanded="false">
       <param name="id_in" argument="-cal:id_in" type="data" format="featurexml,idxml" optional="true" label="Identifications or features whose peptide ID's serve as calibration masses" help=" select featurexml,idxml data sets(s)"/>
       <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" optional="true" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help=" select csv data sets(s)"/>
       <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
       <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/>
-      <param name="model_type" argument="-cal:model_type" type="select" optional="true" label="Type of function to be fitted to the calibration points" help="">
+      <param name="model_type" argument="-cal:model_type" type="select" label="Type of function to be fitted to the calibration points" help="">
         <option value="linear">linear</option>
         <option value="linear_weighted" selected="true">linear_weighted</option>
         <option value="quadratic">quadratic</option>
@@ -139,17 +138,17 @@
     </section>
     <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
       <param name="enabled" argument="-RANSAC:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help=""/>
-      <param name="threshold" argument="-RANSAC:threshold" type="float" optional="true" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
-      <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" optional="true" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
-      <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/>
+      <param name="threshold" argument="-RANSAC:threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
+      <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
+      <param name="iter" argument="-RANSAC:iter" type="integer" value="70" label="Maximal # iterations" help=""/>
     </section>
     <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
-      <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
-      <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
+      <param name="median" argument="-goodness:median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
+      <param name="MAD" argument="-goodness:MAD" type="float" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" 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>
@@ -187,14 +186,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_InternalCalibration_1 -->
+  <tests>
+    <!-- TOPP_InternalCalibration_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
-      <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ppm_match_tolerance" value="25.0"/>
       <param name="ms_level" value="1"/>
       <param name="RT_chunking" value="-1.0"/>
@@ -215,14 +215,17 @@
         <param name="MAD" value="2.0"/>
       </section>
       <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_models" value="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_residuals" value="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <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_InternalCalibration_2 -->
     <test expect_num_outputs="4">
@@ -231,7 +234,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
-      <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ppm_match_tolerance" value="25.0"/>
       <param name="ms_level" value="1 2 3"/>
       <param name="RT_chunking" value="60.0"/>
@@ -252,19 +255,22 @@
         <param name="MAD" value="2.0"/>
       </section>
       <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_models" value="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_residuals" value="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <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 an internal mass recalibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_InternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>