--- a/InternalCalibration.xml	Fri Nov 06 19:50:19 2020 +0000
+++ b/InternalCalibration.xml	Thu Dec 01 19:14:27 2022 +0000
@@ -1,13 +1,11 @@
 <?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]-->
-<tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Applies an internal mass recalibration.</description>
   <macros>
     <token name="@EXECUTABLE@">InternalCalibration</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -120,23 +118,23 @@
     <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
-    <param name="ppm_match_tolerance" 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 name="ms_level" 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)">
-      <expand macro="list_integer_valsan"/>
+    <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)">
+      <expand macro="list_integer_valsan" name="ms_level"/>
     </param>
-    <param name="RT_chunking" 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" 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"/>
     <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" display="radio" type="select" optional="false" label="Type of function to be fitted to the calibration points" help="">
+      <param name="model_type" argument="-cal:model_type" type="select" optional="true" 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>
         <option value="quadratic_weighted">quadratic_weighted</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="model_type"/>
       </param>
     </section>
     <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
@@ -150,9 +148,9 @@
       <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=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -189,13 +187,84 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_InternalCalibration"/>
-    <expand macro="manutest_InternalCalibration"/>
+  <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"/>
+      <param name="ppm_match_tolerance" value="25.0"/>
+      <param name="ms_level" value="1"/>
+      <param name="RT_chunking" value="-1.0"/>
+      <section name="cal">
+        <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
+        <param name="lock_require_mono" value="false"/>
+        <param name="lock_require_iso" value="false"/>
+        <param name="model_type" value="linear"/>
+      </section>
+      <section name="RANSAC">
+        <param name="enabled" value="true"/>
+        <param name="threshold" value="1.0"/>
+        <param name="pc_inliers" value="30"/>
+        <param name="iter" value="500"/>
+      </section>
+      <section name="goodness">
+        <param name="median" value="4.0"/>
+        <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"/>
+      <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>
+    </test>
+    <!-- TOPP_InternalCalibration_2 -->
+    <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_2_lockmass.mzML.gz"/>
+      <output name="out" file="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"/>
+      <section name="cal">
+        <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
+        <param name="lock_require_mono" value="true"/>
+        <param name="lock_require_iso" value="false"/>
+        <param name="model_type" value="linear"/>
+      </section>
+      <section name="RANSAC">
+        <param name="enabled" value="false"/>
+        <param name="threshold" value="10.0"/>
+        <param name="pc_inliers" value="30"/>
+        <param name="iter" value="70"/>
+      </section>
+      <section name="goodness">
+        <param name="median" value="4.0"/>
+        <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"/>
+      <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>
+    </test>
   </tests>
   <help><![CDATA[Applies an internal mass recalibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_InternalCalibration.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>