--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathConfidenceScoring.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,69 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathConfidenceScoring
+
+#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':
+    #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="traml" optional="False" label="Assay library" help="(-lib) "/>
+    <param name="param_trafo" type="data" format="trafoxml" 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_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
+      <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
+      <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" 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</help>
+  <expand macro="references"/>
+</tool>