--- a/LabeledEval.xml	Fri May 17 09:45:56 2019 -0400
+++ b/LabeledEval.xml	Thu Sep 03 16:18:02 2020 +0000
@@ -1,50 +1,76 @@
 <?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: [Utilities]-->
-<tool id="LabeledEval" name="LabeledEval" version="2.3.0">
+<tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
   <macros>
     <token name="@EXECUTABLE@">LabeledEval</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[LabeledEval
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir truth &&
+ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
+
+## Main program call
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_truth:
-  -truth $param_truth
-#end if
-#if $param_rt_tol:
-  -rt_tol $param_rt_tol
-#end if
-#if $param_mz_tol:
-  -mz_tol $param_mz_tol
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-&gt; $param_stdout
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-truth
+'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
+| tee '$stdout'
+
+## Postprocessing
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="featurexml" optional="False" label="Feature result file" help="(-in) "/>
-    <param name="param_truth" type="data" format="consensusxml" optional="False" label="Expected result file" help="(-truth) "/>
-    <param name="param_rt_tol" type="float" value="20.0" label="Maximum allowed retention time deviation" help="(-rt_tol) "/>
-    <param name="param_mz_tol" type="float" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help="(-mz_tol) "/>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
+    <param name="truth" argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
+    <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
+    <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_stdout" format="txt" label="Output from stdout"/>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help> Evaluation tool for isotope-labeled quantitation experiments.
+  <tests>
+    <expand macro="autotest_LabeledEval"/>
+    <expand macro="manutest_LabeledEval"/>
+  </tests>
+  <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_LabeledEval.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_LabeledEval.html]]></help>
+  <expand macro="references"/>
 </tool>