--- a/IDRipper.xml	Fri Nov 06 20:00:01 2020 +0000
+++ b/IDRipper.xml	Thu Dec 01 19:15:32 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: [File Handling]-->
-<tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
-  <description>Split protein/peptide identification file into several files according to annotated file origin.</description>
+<tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description>
   <macros>
     <token name="@EXECUTABLE@">IDRipper</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -18,7 +16,7 @@
 ## Preprocessing
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out_path &&
+mkdir out &&
 
 ## Main program call
 
@@ -28,8 +26,8 @@
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out_path
-out_path/
+-out
+out/
 
 ## Postprocessing
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -40,11 +38,13 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
+    <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/>
+    <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/>
     <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">
@@ -52,20 +52,91 @@
     </param>
   </inputs>
   <outputs>
-    <collection type="list" name="out_path" label="${tool.name} on ${on_string}: out_path">
-      <discover_datasets directory="out_path" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
+      <discover_datasets directory="out" recurse="true" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_IDRipper"/>
-    <expand macro="manutest_IDRipper"/>
-  </tests>
-  <help><![CDATA[Split protein/peptide identification file into several files according to annotated file origin.
+  <tests><!-- TOPP_IDRipper_1 -->
+    <!-- TOPP_IDRipper_2 -->
+    <!-- TOPP_IDRipper_2a -->
+    <!-- TOPP_IDRipper_3 -->
+  <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="IDRipper_1_input.idXML"/>
+      <output_collection name="out" count="2">
+        <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
+        <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
+      </output_collection>
+      <param name="numeric_filenames" value="false"/>
+      <param name="split_ident_runs" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="IDRipper_2_input.idXML"/>
+      <output_collection name="out" count="3">
+        <element name="IDRipper_2_input_idXML_0_0" file="IDRipper_2_input_0_0.idXML" ftype="idxml"/>
+        <element name="IDRipper_2_input_idXML_1_0" file="IDRipper_2_input_1_0.idXML" ftype="idxml"/>
+        <element name="IDRipper_2_input_idXML_2_1" file="IDRipper_2_input_2_1.idXML" ftype="idxml"/>
+      </output_collection>
+      <param name="numeric_filenames" value="true"/>
+      <param name="split_ident_runs" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="IDRipper_2_input.idXML"/>
+      <output_collection name="out" count="2">
+        <element name="IDRipper_2_input_idXML_0" file="IDRipper_2a_output_0.idXML" ftype="idxml"/>
+        <element name="IDRipper_2_input_idXML_1" file="IDRipper_2a_output_1.idXML" ftype="idxml"/>
+      </output_collection>
+      <param name="numeric_filenames" value="true"/>
+      <param name="split_ident_runs" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="IDRipper_3_output.idXML"/>
+      <output_collection name="out" count="2">
+        <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/>
+        <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/>
+      </output_collection>
+      <param name="numeric_filenames" value="false"/>
+      <param name="split_ident_runs" value="false"/>
+      <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[Split protein/peptide identification file into several files according to identification run and annotated file origin.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDRipper.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help>
   <expand macro="references"/>
 </tool>