--- a/FeatureLinkerLabeled.xml	Fri May 17 09:50:16 2019 -0400
+++ b/FeatureLinkerLabeled.xml	Wed Sep 09 12:43:02 2020 +0000
@@ -1,93 +1,81 @@
 <?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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.3.0">
+<tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Groups corresponding isotope-labeled features in a feature map.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerLabeled</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[FeatureLinkerLabeled
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_rt_estimate:
-  -algorithm:rt_estimate
-  #if " " in str($param_algorithm_rt_estimate):
-    "$param_algorithm_rt_estimate"
-  #else
-    $param_algorithm_rt_estimate
-  #end if
-#end if
-#if $param_algorithm_rt_pair_dist:
-  -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
-#end if
-#if $param_algorithm_rt_dev_low:
-  -algorithm:rt_dev_low $param_algorithm_rt_dev_low
-#end if
-#if $param_algorithm_rt_dev_high:
-  -algorithm:rt_dev_high $param_algorithm_rt_dev_high
-#end if
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("consensusxml")}'
 
-#if $rep_param_algorithm_mz_pair_dists:
--algorithm:mz_pair_dists
-  #for token in $rep_param_algorithm_mz_pair_dists:
-    #if " " in str(token):
-      "$token.param_algorithm_mz_pair_dists"
-    #else
-      $token.param_algorithm_mz_pair_dists
-    #end if
-  #end for
-#end if
-#if $param_algorithm_mz_dev:
-  -algorithm:mz_dev $param_algorithm_mz_dev
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_mrm:
-  -algorithm:mrm
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
+#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="Input file" help="(-in) "/>
-    <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance">
-      <option value="true" selected="true">true</option>
-      <option value="false">false</option>
+    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
+      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
+      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
+      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
+      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <expand macro="list_float_valsan"/>
+      </param>
+      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
+      <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
+    </section>
+    <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>
-    <param name="param_algorithm_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist) "/>
-    <param name="param_algorithm_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low) "/>
-    <param name="param_algorithm_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high) "/>
-    <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
-      <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
-    </repeat>
-    <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
-    <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="param_algorithm_mrm" display="radio" type="boolean" truevalue="-algorithm:mrm" falsevalue="" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="consensusxml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Groups corresponding isotope-labeled features in a feature map.
+  <tests>
+    <expand macro="autotest_FeatureLinkerLabeled"/>
+    <expand macro="manutest_FeatureLinkerLabeled"/>
+  </tests>
+  <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerLabeled.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerLabeled.html]]></help>
+  <expand macro="references"/>
 </tool>