--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathConfidenceScoring.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,49 @@
+<?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
+
+-in ${param_in}
+-lib ${param_lib}
+-out ${param_out}
+-trafo ${param_trafo}
+-decoys ${param_decoys}
+-transitions ${param_transitions}
+-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}
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html
+
+@REFERENCES@
+</help>
+</tool>