--- a/ProteinInference.xml	Thu Sep 24 09:03:45 2020 +0000
+++ b/ProteinInference.xml	Tue Oct 13 19:58:27 2020 +0000
@@ -50,6 +50,7 @@
     <param name="annotate_indist_groups" argument="-annotate_indist_groups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If you want to annotate indistinguishable protein groups, either for reporting or for group based quant" help="later. Only works with a single ID run in the file"/>
     <section name="Merging" title="" help="" expanded="false">
       <param name="annotate_origin" argument="-Merging:annotate_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from" help=""/>
+      <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/>
     </section>
     <section name="Algorithm" title="" help="" expanded="false">
       <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
@@ -73,12 +74,12 @@
       </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="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>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -95,6 +96,6 @@
   <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_ProteinInference.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinInference.html]]></help>
   <expand macro="references"/>
 </tool>