--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/InternalCalibration.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,81 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="InternalCalibration" name="InternalCalibration" version="2.0.0">
+  <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
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_ref_peaks:
+  -ref_peaks $param_ref_peaks
+#end if
+#if $param_type:
+  -type
+  #if " " in str($param_type):
+    "$param_type"
+  #else
+    $param_type
+  #end if
+#end if
+#if $param_trafo:
+  -trafo $param_trafo
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_algorithm_mz_tolerance:
+  -algorithm:mz_tolerance $param_algorithm_mz_tolerance
+#end if
+#if $param_algorithm_mz_tolerance_unit:
+  -algorithm:mz_tolerance_unit
+  #if " " in str($param_algorithm_mz_tolerance_unit):
+    "$param_algorithm_mz_tolerance_unit"
+  #else
+    $param_algorithm_mz_tolerance_unit
+  #end if
+#end if
+#if $param_algorithm_rt_tolerance:
+  -algorithm:rt_tolerance $param_algorithm_rt_tolerance
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featurexml,mzml" 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_algorithm_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_algorithm_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_algorithm_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt" help="(-rt_tolerance) "/>
+    <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" metadata_source="param_in" format="input"/>
+    <data name="param_trafo" format="trafoxml"/>
+  </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</help>
+  <expand macro="references"/>
+</tool>