--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathDIAPreScoring.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathDIAPreScoring
+
+#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="traml" optional="False" label="transition file" help="(-tr) "/>
+    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <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) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Scoring spectra using the DIA scores.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help>
+  <expand macro="references"/>
+</tool>