--- a/SeedListGenerator.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/SeedListGenerator.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,33 +1,53 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="SeedListGenerator" name="SeedListGenerator" version="1.12.0">
-  <description>Generates seed lists for feature detection.</description>
-  <macros>
-    <token name="@EXECUTABLE@">SeedListGenerator</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>SeedListGenerator
+<?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: [Quantitation]-->
+  <tool id="SeedListGenerator" name="SeedListGenerator" version="2.0.0">
+    <description>Generates seed lists for feature detection.</description>
+    <macros>
+      <token name="@EXECUTABLE@">SeedListGenerator</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>SeedListGenerator
+
+#if $param_in:
+  -in $param_in
+#end if
 
--in ${param_in}
--out ${param_out}
-${param_use_peptide_mass}
--threads \${GALAXY_SLOTS:-24} 
+#if $rep_param_out:
+-out
+  #for token in $rep_param_out:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_out&quot;
+    #else
+      $token.param_out
+    #end if
+  #end for
+#end if
+#if $param_use_peptide_mass:
+  -use_peptide_mass
+#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" type="data" format="mzML,idXML,featureXML,consensusXML" optional="False" label="Input file (see below for details)" help="(-in)"/>
-    <param name="param_use_peptide_mass" type="boolean" truevalue="-use_peptide_mass true" falsevalue="-use_peptide_mass false" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file(s)" format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Generates seed lists for feature detection.
+    <inputs>
+      <param format="xml,consensusxml,mzml" help="(-in) " label="Input file (see below for details)" name="param_in" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-use_peptide_mass) " label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" name="param_use_peptide_mass" optional="True" truevalue="-use_peptide_mass" type="boolean"/>
+      <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="xml" name="param_out"/>
+    </outputs>
+    <help>Generates seed lists for feature detection.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html</help>
+  </tool>