--- a/SequenceCoverageCalculator.xml	Tue Mar 20 14:50:30 2018 -0400
+++ b/SequenceCoverageCalculator.xml	Wed May 15 08:23:08 2019 -0400
@@ -1,32 +1,39 @@
 <?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]-->
-<tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0">
+<tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0+galaxy1">
   <description>Prints information about idXML files.</description>
   <macros>
     <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
     <import>macros.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>SequenceCoverageCalculator
-
+  <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator
 #if $param_in_database:
-  -in_database $param_in_database
+  -in_database '$param_in_database'
 #end if
 #if $param_in_peptides:
-  -in_peptides $param_in_peptides
-#end if
-#if $param_out:
-  -out $param_out
+  -in_peptides '$param_in_peptides'
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
   -force
 #end if
 #end if
-</command>
+
+## fix output (https://github.com/OpenMS/OpenMS/issues/3605)
+## - add header
+## - remove reformat data
+## - remove summary info
+## - print summary info to stdout
+| sed '1i#protein\tcoverage%\t#unique hits' 
+| sed 's/^\(.*\)(coverage%, #unique hits): \([0-9.]\+\)%, \([0-9]\+\)/\1\t\2\t\3/'
+| tee tmpout 
+| egrep -v  "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" > '$param_out'
+## 
+&& cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took"
+]]></command>
   <inputs>
     <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database) "/>
     <param name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/>
@@ -35,10 +42,19 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="txt"/>
+    <data name="param_out" format="tabular"/>
   </outputs>
+  <tests>
+	  <test>
+    <param name="param_in_database" ftype="fasta" value="OpenPepXL_input.fasta"/>
+    <!-- generated with: IDFilter -best:strict -in ~/projects/OpenMS/src/tests/topp/OpenPepXL_output.idXML -out SequenceCoverageCalculator.idXML-->
+    <param name="param_in_peptides" ftype="idxml" value="SequenceCoverageCalculator.idXML" />
+    <output name="param_out" file="SequenceCoverageCalculator.tsv" ftype="tabular" />
+    </test>
+  </tests>
   <help>Prints information about idXML files.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help>
+  <expand macro="references"/>
 </tool>