--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MapAlignmentEvaluation.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,72 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
+  <description>Evaluates alignment results against a ground truth.</description>
+  <macros>
+    <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MapAlignmentEvaluation
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_gt:
+  -gt $param_gt
+#end if
+#if $param_type:
+  -type
+  #if " " in str($param_type):
+    "$param_type"
+  #else
+    $param_type
+  #end if
+#end if
+#if $param_rt_dev:
+  -rt_dev $param_rt_dev
+#end if
+#if $param_mz_dev:
+  -mz_dev $param_mz_dev
+#end if
+#if $param_int_dev:
+  -int_dev $param_int_dev
+#end if
+#if $param_use_charge:
+  -use_charge
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+&gt; $param_stdout
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="consensusxml" optional="False" label="input file: tool" help="(-in) "/>
+    <param name="param_gt" type="data" format="consensusxml" optional="False" label="input file: ground truth" help="(-gt) "/>
+    <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type) ">
+      <option value="precision">precision</option>
+      <option value="recall">recall</option>
+      <option value="F1">F1</option>
+    </param>
+    <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev) "/>
+    <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev) "/>
+    <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev) "/>
+    <param name="param_use_charge" type="boolean" truevalue="-use_charge" falsevalue="" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical" help="(-use_charge) "/>
+    <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_stdout" format="text" label="Output from stdout"/>
+  </outputs>
+  <help>**What it does**
+
+Evaluates alignment results against a ground truth.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html</help>
+  <expand macro="references"/>
+</tool>