--- a/OpenSwathConfidenceScoring.xml	Fri May 17 10:02:24 2019 -0400
+++ b/OpenSwathConfidenceScoring.xml	Thu Aug 27 19:49:07 2020 -0400
@@ -1,68 +1,91 @@
 <?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: [Targeted Experiments]-->
-<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.3.0">
+<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Compute confidence scores for OpenSwath results</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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[OpenSwathConfidenceScoring
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_lib:
-  -lib $param_lib
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_trafo:
-  -trafo $param_trafo
-#end if
-#if $param_decoys:
-  -decoys $param_decoys
-#end if
-#if $param_transitions:
-  -transitions $param_transitions
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir lib &&
+ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
+mkdir out &&
+#if $trafo:
+  mkdir trafo &&
+  ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
 #end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_GLM_intercept:
-  -GLM:intercept $adv_opts.param_GLM_intercept
-#end if
-    #if $adv_opts.param_GLM_delta_rt:
-  -GLM:delta_rt $adv_opts.param_GLM_delta_rt
-#end if
-    #if $adv_opts.param_GLM_dist_int:
-  -GLM:dist_int $adv_opts.param_GLM_dist_int
-#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-lib
+'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
+-out
+'out/output.${gxy2omsext("featurexml")}'
+#if $trafo:
+  -trafo
+  'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)'
 #end if
-]]></command>
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("featurexml")}' '$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 (OpenSwath results)" help="(-in) "/>
-    <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/>
-    <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/>
-    <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys) "/>
-    <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help="(-transitions) "/>
-    <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_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
-      <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
-      <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
+    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
+    <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
+    <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
+    <param name="decoys" argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
+    <param name="transitions" argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
+    <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
+      <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
+      <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
+      <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" 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>
   </inputs>
   <outputs>
-    <data name="param_out" format="featurexml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Compute confidence scores for OpenSwath results
+  <tests>
+    <expand macro="autotest_OpenSwathConfidenceScoring"/>
+    <expand macro="manutest_OpenSwathConfidenceScoring"/>
+  </tests>
+  <help><![CDATA[Compute confidence scores for OpenSwath results
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathConfidenceScoring.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathConfidenceScoring.html]]></help>
+  <expand macro="references"/>
 </tool>