--- a/OpenSwathRewriteToFeatureXML.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathRewriteToFeatureXML.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,35 +1,49 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="1.12.0">
-  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
-  <macros>
-    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>OpenSwathRewriteToFeatureXML
+<?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: [Targeted Experiments]-->
+  <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
+    <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
+    <macros>
+      <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>OpenSwathRewriteToFeatureXML
 
--csv ${param_csv}
--featureXML ${param_featureXML}
--out ${param_out}
--FDR_cutoff ${param_FDR_cutoff}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_csv:
+  -csv $param_csv
+#end if
+#if $param_featureXML:
+  -featureXML $param_featureXML
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_FDR_cutoff:
+  -FDR_cutoff $param_FDR_cutoff
+#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_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv)"/>
-    <param name="param_featureXML" type="data" format="featureXML" optional="False" label="input featureXML file" help="(-featureXML)"/>
-    <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" help="(-FDR_cutoff)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output featureXML file" format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Combines featureXML and mProphet tsv to FDR filtered featureXML.
+    <inputs>
+      <param format="tabular" help="(-csv) " label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" name="param_csv" optional="True" type="data"/>
+      <param format="xml" help="(-featureXML) " label="input featureXML file" name="param_featureXML" optional="False" type="data"/>
+      <param help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" label="FDR cutoff (" name="param_FDR_cutoff" type="float" value="-1.0"/>
+      <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>Combines featureXML and mProphet tsv to FDR filtered featureXML.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html</help>
+  </tool>