--- a/MetaboliteSpectralMatcher.xml	Fri May 17 09:49:40 2019 -0400
+++ b/MetaboliteSpectralMatcher.xml	Thu Sep 03 16:24:57 2020 +0000
@@ -1,88 +1,94 @@
 <?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="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.3.0">
+<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Perform a spectral library search.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</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[MetaboliteSpectralMatcher
+  <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($in.ext)' &&
+mkdir database &&
+ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-database
+'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
+-out
+'out/output.${gxy2omsext("mztab")}'
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_database:
-  -database $param_database
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_prec_mass_error_value:
-  -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
-#end if
-#if $param_algorithm_frag_mass_error_value:
-  -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
-#end if
-#if $param_algorithm_mass_error_unit:
-  -algorithm:mass_error_unit
-  #if " " in str($param_algorithm_mass_error_unit):
-    "$param_algorithm_mass_error_unit"
-  #else
-    $param_algorithm_mass_error_unit
-  #end if
-#end if
-#if $param_algorithm_report_mode:
-  -algorithm:report_mode
-  #if " " in str($param_algorithm_report_mode):
-    "$param_algorithm_report_mode"
-  #else
-    $param_algorithm_report_mode
-  #end if
-#end if
-#if $param_algorithm_ionization_mode:
-  -algorithm:ionization_mode
-  #if " " in str($param_algorithm_ionization_mode):
-    "$param_algorithm_ionization_mode"
-  #else
-    $param_algorithm_ionization_mode
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("mztab")}' '$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="mzml" optional="False" label="Input spectra" help="(-in) "/>
-    <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/>
-    <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
-    <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
-    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
-      <option value="ppm" selected="true">ppm</option>
-      <option value="Da">Da</option>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
+    <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
+      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
+        <option value="ppm" selected="true">ppm</option>
+        <option value="Da">Da</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="report_mode" argument="-algorithm:report_mode" display="radio" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
+        <option value="top3" selected="true">top3</option>
+        <option value="best">best</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help="">
+        <option value="positive" selected="true">positive</option>
+        <option value="negative">negative</option>
+        <expand macro="list_string_san"/>
+      </param>
+    </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_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
-      <option value="top3" selected="true">top3</option>
-      <option value="best">best</option>
-    </param>
-    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
-      <option value="positive" selected="true">positive</option>
-      <option value="negative">negative</option>
-    </param>
-    <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) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="tabular"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Perform a spectral library search.
+  <tests>
+    <expand macro="autotest_MetaboliteSpectralMatcher"/>
+    <expand macro="manutest_MetaboliteSpectralMatcher"/>
+  </tests>
+  <help><![CDATA[Perform a spectral library search.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MetaboliteSpectralMatcher.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_MetaboliteSpectralMatcher.html]]></help>
+  <expand macro="references"/>
 </tool>