--- a/OpenSwathConfidenceScoring.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathConfidenceScoring.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,49 +1,69 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="1.12.0">
-  <description>Compute confidence scores for OpenSwath results</description>
-  <macros>
-    <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>OpenSwathConfidenceScoring
+<?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="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.0.0">
+    <description>Compute confidence scores for OpenSwath results</description>
+    <macros>
+      <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>OpenSwathConfidenceScoring
 
--in ${param_in}
--lib ${param_lib}
--out ${param_out}
--trafo ${param_trafo}
--decoys ${param_decoys}
--transitions ${param_transitions}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_lib:
+  -lib $param_lib
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_trafo:
+  -trafo $param_trafo
+#end if
+#if $param_decoys:
+  -decoys $param_decoys
+#end if
+#if $param_transitions:
+  -transitions $param_transitions
+#end if
+-threads \${GALAXY_SLOTS:-24}
 #if $adv_opts.adv_opts_selector=='advanced':
-    -GLM:intercept ${adv_opts.param_intercept}
-    -GLM:delta_rt ${adv_opts.param_delta_rt}
-    -GLM:dist_int ${adv_opts.param_dist_int}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_GLM_intercept:
+  -GLM:intercept $adv_opts.param_GLM_intercept
+#end if
+    #if $adv_opts.param_GLM_delta_rt:
+  -GLM:delta_rt $adv_opts.param_GLM_delta_rt
+#end if
+    #if $adv_opts.param_GLM_dist_int:
+  -GLM:dist_int $adv_opts.param_GLM_dist_int
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML" optional="False" label="Input file (OpenSwath results)" help="(-in)"/>
-    <param name="param_lib" type="data" format="" optional="False" label="Assay library" help="(-lib)"/>
-    <param name="param_trafo" type="data" format="" optional="True" label="Retention time transformation" help="(-trafo)"/>
-    <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys)"/>
-    <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help="(-transitions)"/>
-    <expand macro="advanced_options">
-      <param name="param_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept)"/>
-      <param name="param_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt)"/>
-      <param name="param_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file (results with confidence scores)" format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Compute confidence scores for OpenSwath results
+    <inputs>
+      <param format="xml" help="(-in) " label="Input file (OpenSwath results)" name="param_in" optional="False" type="data"/>
+      <param format="traml" help="(-lib) " label="Assay library" name="param_lib" optional="False" type="data"/>
+      <param format="trafoxml" help="(-trafo) " label="Retention time transformation" name="param_trafo" optional="True" type="data"/>
+      <param help="(-decoys) " label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" min="0" name="param_decoys" optional="True" type="integer" value="1000"/>
+      <param help="(-transitions) " label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" min="0" name="param_transitions" optional="True" type="integer" value="6"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-intercept) " label="Intercept term" name="param_GLM_intercept" type="float" value="3.87333466"/>
+        <param help="(-delta_rt) " label="Coefficient of retention time difference" name="param_GLM_delta_rt" type="float" value="-0.02898629"/>
+        <param help="(-dist_int) " label="Coefficient of intensity distance" name="param_GLM_dist_int" type="float" value="-7.75880768"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>Compute confidence scores for OpenSwath results
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help>
+  </tool>