--- a/SequenceCoverageCalculator.xml	Fri May 17 09:57:17 2019 -0400
+++ b/SequenceCoverageCalculator.xml	Wed Sep 09 12:44:46 2020 +0000
@@ -1,60 +1,75 @@
 <?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+galaxy1">
+<tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Prints information about idXML files.</description>
   <macros>
     <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator
-#if $param_in_database:
-  -in_database '$param_in_database'
-#end if
-#if $param_in_peptides:
-  -in_peptides '$param_in_peptides'
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in_database &&
+ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
+mkdir in_peptides &&
+ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
+mkdir out &&
+
+## Main program call
 
-## 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" > '$param_out'
-## 
-&& cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took"
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in_database
+'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)'
+-in_peptides
+'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)'
+-out
+'out/output.${gxy2omsext("txt")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("txt")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <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) "/>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="in_database" argument="-in_database" type="data" format="fasta" optional="false" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
+    <param name="in_peptides" argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
+    <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="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">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="tabular"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
   <tests>
-	  <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>
+    <expand macro="autotest_SequenceCoverageCalculator"/>
+    <expand macro="manutest_SequenceCoverageCalculator"/>
   </tests>
-  <help>Prints information about idXML files.
+  <help><![CDATA[Prints information about idXML files.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_SequenceCoverageCalculator.html]]></help>
   <expand macro="references"/>
 </tool>