--- a/OpenSwathFeatureXMLToTSV.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathFeatureXMLToTSV.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,37 +1,68 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="1.12.0">
-  <description>Converts a featureXML to a mProphet tsv.</description>
-  <macros>
-    <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>OpenSwathFeatureXMLToTSV
+<?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="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
+    <description>Converts a featureXML to a mProphet tsv.</description>
+    <macros>
+      <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>OpenSwathFeatureXMLToTSV
 
--in ${param_in}
--tr ${param_tr}
--out ${param_out}
-${param_short_format}
--best_scoring_peptide ${param_best_scoring_peptide}
--threads \${GALAXY_SLOTS:-24} 
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_short_format:
+  -short_format
+#end if
+#if $param_best_scoring_peptide:
+  -best_scoring_peptide     &quot;$param_best_scoring_peptide&quot;
+#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="featureXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
-    <param name="param_tr" type="data" format="" optional="False" label="TraML transition file" help="(-tr)"/>
-    <param name="param_short_format" type="boolean" truevalue="-short_format true" falsevalue="-short_format false" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)." help="(-short_format)"/>
-    <param name="param_best_scoring_peptide" type="text" size="20" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="tsv output file (mProphet compatible)" format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Converts a featureXML to a mProphet tsv.
+    <inputs>
+      <param format="xml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param format="traml" help="(-tr) " label="TraML transition file" name="param_tr" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-short_format) " label="Whether to write short (one peptide per line) or long format (one transition per line)" name="param_short_format" optional="True" truevalue="-short_format" type="boolean"/>
+      <param help="(-best_scoring_peptide) " label="If only the best scoring feature per peptide should be printed, give the variable name" name="param_best_scoring_peptide" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <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="tabular" name="param_out"/>
+    </outputs>
+    <help>Converts a featureXML to a mProphet tsv.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
+  </tool>