--- a/PSMFeatureExtractor.xml	Thu Dec 01 19:01:06 2022 +0000
+++ b/PSMFeatureExtractor.xml	Fri Jun 14 21:40:34 2024 +0000
@@ -1,8 +1,7 @@
-<?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]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes extra features for each input PSM.</description>
+  <description>Computes extra features for each input PSM</description>
   <macros>
     <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,15 +53,16 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,mzid" multiple="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,mzid" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
@@ -76,7 +76,7 @@
       <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>
       <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>
       <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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -94,34 +94,89 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-  </test>
-  <!-- test for the batch conditional crated for data parameters with multiple="true" -->
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_select" value="yes"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
-  </test>
-</tests>
+  <tests>
+    <!-- TOPP_PSMFeatureExtractor_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="true"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="multiple_search_engines" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_PSMFeatureExtractor_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="true"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_2_out.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <param name="out_type" value="mzid"/>
+      <param name="multiple_search_engines" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_PSMFeatureExtractor_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="false"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="multiple_search_engines" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+  </tests>
   <help><![CDATA[Computes extra features for each input PSM.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PSMFeatureExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PSMFeatureExtractor.html]]></help>
   <expand macro="references"/>
 </tool>