--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RTEvaluation.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="RTEvaluation" name="RTEvaluation" version="2.0.0">
+  <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
+  <macros>
+    <token name="@EXECUTABLE@">RTEvaluation</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>RTEvaluation
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_sequences_file:
+  -sequences_file $param_sequences_file
+#end if
+#if $param_latex:
+  -latex
+#end if
+#if $param_p_value_dim_1:
+  -p_value_dim_1 $param_p_value_dim_1
+#end if
+#if $param_p_value_dim_2:
+  -p_value_dim_2 $param_p_value_dim_2
+#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_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-sequences_file) &lt;br&gt;All peptides that are not a substring of a sequence in this file are considered as false"/>
+    <param name="param_latex" type="boolean" truevalue="-latex" falsevalue="" checked="false" optional="True" label="indicates whether the output file format of the table should be latex or csv" help="(-latex) "/>
+    <param name="param_p_value_dim_1" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Significance level of first dimension RT filte" help="(-p_value_dim_1) "/>
+    <param name="param_p_value_dim_2" type="float" min="0.0" max="1.0" optional="True" value="0.05" label="Significance level of second dimension RT filte" help="(-p_value_dim_2) "/>
+    <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**
+
+Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html</help>
+  <expand macro="references"/>
+</tool>