--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MapRTTransformer.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,58 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MapRTTransformer" name="MapRTTransformer" version="1.12.0">
+  <description>Applies retention time transformations to maps.</description>
+  <macros>
+    <token name="@EXECUTABLE@">MapRTTransformer</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MapRTTransformer
+
+-in ${param_in}
+-out ${param_out}
+-trafo_in ${param_trafo_in}
+-trafo_out ${param_trafo_out}
+${param_invert}
+-threads \${GALAXY_SLOTS:-24} 
+-model:type ${param_type}
+${param_symmetric_regression}
+-model:interpolated:interpolation_type ${param_interpolation_type}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML,featureXML,consensusXML,idXML" optional="True" size="20" label="Input files to transform (separated by blanks)" help="(-in)"/>
+    <param name="param_trafo_in" type="data" format="" optional="False" size="20" label="Transformations to apply (files separated by blanks)" help="(-trafo_in)"/>
+    <param name="param_invert" type="boolean" truevalue="-invert true" falsevalue="-invert false" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert)"/>
+    <param name="param_type" type="select" optional="True" value="none" label="Type of model" help="(-type)">
+      <option value="none">none</option>
+      <option value="linear">linear</option>
+      <option value="b_spline">b_spline</option>
+      <option value="interpolated">interpolated</option>
+    </param>
+    <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
+    <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
+      <option value="linear">linear</option>
+      <option value="cspline">cspline</option>
+      <option value="akima">akima</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together." format="idXML">
+      <change_format>
+        <when input="param_out_type" value="mzML" format="mzML"/>
+        <when input="param_out_type" value="featureXML" format="featureXML"/>
+        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
+      </change_format>
+    </data>
+    <data name="param_trafo_out" label="Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together." format="data"/>
+  </outputs>
+  <help>**What it does**
+
+Applies retention time transformations to maps.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html
+
+@REFERENCES@
+</help>
+</tool>