--- a/MassCalculator.xml	Wed Sep 23 14:57:35 2020 +0000
+++ b/MassCalculator.xml	Tue Oct 13 20:13:07 2020 +0000
@@ -36,7 +36,7 @@
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  'out/output.${gxy2omsext("txt")}'
+  'out/output.${gxy2omsext("csv")}'
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -44,7 +44,7 @@
 
 ## Postprocessing
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("txt")}' '$out'
+  && mv 'out/output.${gxy2omsext("csv")}' '$out'
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -54,7 +54,7 @@
     <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="txt" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
+    <param name="in" argument="-in" type="data" format="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/>
     <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" 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"/>
@@ -87,18 +87,18 @@
       <expand macro="list_string_san"/>
     </param>
     <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="false">
-      <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
@@ -115,6 +115,6 @@
   <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_MassCalculator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MassCalculator.html]]></help>
   <expand macro="references"/>
 </tool>