--- a/OpenSwathDIAPreScoring.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathDIAPreScoring.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,35 +1,57 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="1.12.0">
-  <description>Scoring spectra using the DIA scores.</description>
-  <macros>
-    <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>OpenSwathDIAPreScoring
+<?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="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.0.0">
+    <description>Scoring spectra using the DIA scores.</description>
+    <macros>
+      <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>OpenSwathDIAPreScoring
 
--tr ${param_tr}
--out ${param_out}
--swath_files ${param_swath_files}
--min_upper_edge_dist ${param_min_upper_edge_dist}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-swath_files
+  #for token in $param_swath_files:
+    $token
+  #end for
+#if $param_min_upper_edge_dist:
+  -min_upper_edge_dist $param_min_upper_edge_dist
+#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_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
-    <param name="param_swath_files" type="data" format="mzML" optional="True" size="20" label="Swath files that were used to extract the transitions. If present, SWATH specific scoring will be applied." help="(-swath_files)"/>
-    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Scoring spectra using the DIA scores.
+    <inputs>
+      <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/>
+      <param format="mzml" help="(-swath_files) If present, SWATH specific scoring will be applied" label="Swath files that were used to extract the transitions" multiple="true" name="param_swath_files" optional="True" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" name="param_min_upper_edge_dist" type="float" value="0.0"/>
+      <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="tabular" name="param_out"/>
+    </outputs>
+    <help>Scoring spectra using the DIA scores.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help>
+  </tool>