--- a/MascotAdapter.xml	Fri Nov 06 20:12:23 2020 +0000
+++ b/MascotAdapter.xml	Thu Dec 01 19:12:19 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: [Identification]-->
-<tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Annotates MS/MS spectra using Mascot.</description>
   <macros>
     <token name="@EXECUTABLE@">MascotAdapter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,18 +39,18 @@
     <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
-    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
+    <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
+    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
       <option value="idXML">idxml</option>
       <option value="mgf">mgf</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
+      <expand macro="list_string_san" name="instrument"/>
     </param>
-    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
-    <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
-    <param name="taxonomy" argument="-taxonomy" type="select" optional="false" label="the taxonomy" help="">
+    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
+    <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
+    <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help="">
       <option value="All entries" selected="true">All entries</option>
       <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
       <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
@@ -118,27 +116,27 @@
       <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
       <option value=". . unclassified">. . unclassified</option>
       <option value=". . Species information unavailable">. . Species information unavailable</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="taxonomy"/>
     </param>
-    <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-      <expand macro="list_string_val"/>
-      <expand macro="list_string_san"/>
+    <param argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_string_val" name="modifications"/>
+      <expand macro="list_string_san" name="modifications"/>
     </param>
-    <param name="variable_modifications" argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-      <expand macro="list_string_val"/>
-      <expand macro="list_string_san"/>
+    <param argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_string_val" name="variable_modifications"/>
+      <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param name="charges" argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-      <expand macro="list_string_val"/>
-      <expand macro="list_string_san"/>
+    <param argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_string_val" name="charges"/>
+      <expand macro="list_string_san" name="charges"/>
     </param>
-    <param name="db" argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
+      <expand macro="list_string_san" name="db"/>
     </param>
-    <param name="hits" argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
+      <expand macro="list_string_san" name="hits"/>
     </param>
-    <param name="cleavage" argument="-cleavage" type="select" optional="false" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
+    <param argument="-cleavage" type="select" optional="true" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
       <option value="Trypsin" selected="true">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
       <option value="Asp-N">Asp-N</option>
@@ -158,30 +156,30 @@
       <option value="semiTrypsin">semiTrypsin</option>
       <option value="LysC+AspN">LysC+AspN</option>
       <option value="None">None</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="cleavage"/>
     </param>
-    <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
-    <param name="sig_threshold" argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
-    <param name="pep_homol" argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
-    <param name="pep_ident" argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
-    <param name="pep_rank" argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
-    <param name="prot_score" argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
-    <param name="pep_score" argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
-    <param name="pep_exp_z" argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
-    <param name="show_unassigned" argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
-    <param name="first_dim_rt" argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
-    <param name="boundary" argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
+    <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
+    <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
+    <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
+    <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
+    <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
+    <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
+    <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
+    <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
+    <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
+    <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
+      <expand macro="list_string_san" name="boundary"/>
     </param>
-    <param name="mass_type" argument="-mass_type" display="radio" type="select" optional="false" label="mass type" help="">
+    <param argument="-mass_type" type="select" optional="true" label="mass type" help="">
       <option value="Monoisotopic" selected="true">Monoisotopic</option>
       <option value="Average">Average</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="mass_type"/>
     </param>
     <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">
@@ -189,9 +187,8 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
       <change_format>
-        <when input="out_type" value="idXML" format="idxml"/>
         <when input="out_type" value="mgf" format="mgf"/>
       </change_format>
     </data>
@@ -199,13 +196,86 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MascotAdapter"/>
-    <expand macro="manutest_MascotAdapter"/>
+  <tests><!-- TOPP_MascotAdapter_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MascotAdapter_1_input.mzData"/>
+      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
+      <param name="out_type" value="mgf"/>
+      <param name="instrument" value="ESI-TRAP"/>
+      <param name="precursor_mass_tolerance" value="1.3"/>
+      <param name="peak_mass_tolerance" value="0.3"/>
+      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
+      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
+      <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
+      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
+      <param name="db" value="MSDB"/>
+      <param name="hits" value="AUTO"/>
+      <param name="cleavage" value="Trypsin"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="sig_threshold" value="0.05"/>
+      <param name="pep_homol" value="1.0"/>
+      <param name="pep_ident" value="1.0"/>
+      <param name="pep_rank" value="1"/>
+      <param name="prot_score" value="1.0"/>
+      <param name="pep_score" value="1.0"/>
+      <param name="pep_exp_z" value="1"/>
+      <param name="show_unassigned" value="1"/>
+      <param name="first_dim_rt" value="0.0"/>
+      <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
+      <param name="mass_type" value="Monoisotopic"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MascotAdapter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
+      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="instrument" value="Default"/>
+      <param name="precursor_mass_tolerance" value="2.0"/>
+      <param name="peak_mass_tolerance" value="1.0"/>
+      <param name="taxonomy" value="All entries"/>
+      <param name="modifications" value=""/>
+      <param name="variable_modifications" value=""/>
+      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
+      <param name="db" value="MSDB"/>
+      <param name="hits" value="AUTO"/>
+      <param name="cleavage" value="Trypsin"/>
+      <param name="missed_cleavages" value="0"/>
+      <param name="sig_threshold" value="0.05"/>
+      <param name="pep_homol" value="1.0"/>
+      <param name="pep_ident" value="1.0"/>
+      <param name="pep_rank" value="1"/>
+      <param name="prot_score" value="1.0"/>
+      <param name="pep_score" value="1.0"/>
+      <param name="pep_exp_z" value="1"/>
+      <param name="show_unassigned" value="1"/>
+      <param name="first_dim_rt" value="0.0"/>
+      <param name="boundary" value=""/>
+      <param name="mass_type" value="Monoisotopic"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Annotates MS/MS spectra using Mascot.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help>
   <expand macro="references"/>
 </tool>