--- a/SequenceCoverageCalculator.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/SequenceCoverageCalculator.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,33 +1,45 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="1.12.0">
-  <description>Prints information about idXML files.</description>
-  <macros>
-    <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>SequenceCoverageCalculator
+<?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 CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Utilities]-->
+  <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.0.0">
+    <description>Prints information about idXML files.</description>
+    <macros>
+      <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>SequenceCoverageCalculator
 
--in_database ${param_in_database}
--in_peptides ${param_in_peptides}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
+#if $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
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </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)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Optional text output file. If left out, the output is written to the command line." format="txt"/>
-  </outputs>
-  <help>**What it does**
-
-Prints information about idXML files.
+    <inputs>
+      <param format="fasta" help="(-in_database) " label="input file containing the database in FASTA format" name="param_in_database" optional="False" type="data"/>
+      <param format="xml" help="(-in_peptides) " label="input file containing the identified peptides" name="param_in_peptides" optional="False" type="data"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="txt" name="param_out"/>
+    </outputs>
+    <help>Prints information about idXML files.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SequenceCoverageCalculator.html</help>
+  </tool>