--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/InternalCalibration.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,53 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="InternalCalibration" name="InternalCalibration" version="1.12.0">
+  <description>Applies an internal calibration.</description>
+  <macros>
+    <token name="@EXECUTABLE@">InternalCalibration</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>InternalCalibration
+
+-in ${param_in}
+-out ${param_out}
+-ref_peaks ${param_ref_peaks}
+-type ${param_type}
+-trafo ${param_trafo}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:mz_tolerance ${param_mz_tolerance}
+-algorithm:mz_tolerance_unit ${param_mz_tolerance_unit}
+-algorithm:rt_tolerance ${param_rt_tolerance}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML,featureXML" optional="False" label="input peak file " help="(-in)"/>
+    <param name="param_ref_peaks" type="data" format="tabular,idXML" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks)"/>
+    <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied." help="(-type)">
+      <option value="spectrumwise">spectrumwise</option>
+      <option value="global">global</option>
+    </param>
+    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z." help="(-mz_tolerance)"/>
+    <param name="param_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance." help="(-mz_tolerance_unit)">
+      <option value="Da">Da</option>
+      <option value="ppm">ppm</option>
+    </param>
+    <param name="param_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt." help="(-rt_tolerance)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file " format="featureXML">
+      <change_format>
+        <when input="param_out_type" value="mzML" format="mzML"/>
+      </change_format>
+    </data>
+    <data name="param_trafo" label="output transformation file (only for global calibration)" format="data"/>
+  </outputs>
+  <help>**What it does**
+
+Applies an internal calibration.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html
+
+@REFERENCES@
+</help>
+</tool>