--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInference.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="ProteinInference" name="ProteinInference" version="1.12.0">
+  <description>Protein inference based on the number of identified peptides.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ProteinInference</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ProteinInference
+
+-in ${param_in}
+-out ${param_out}
+-min_peptides_per_protein ${param_min_peptides_per_protein}
+${param_treat_charge_variants_separately}
+${param_treat_modification_variants_separately}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/>
+    <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein)"/>
+    <param name="param_treat_charge_variants_separately" type="boolean" truevalue="-treat_charge_variants_separately true" falsevalue="-treat_charge_variants_separately false" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences." help="(-treat_charge_variants_separately)"/>
+    <param name="param_treat_modification_variants_separately" type="boolean" truevalue="-treat_modification_variants_separately true" falsevalue="-treat_modification_variants_separately false" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences." help="(-treat_modification_variants_separately)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="idXML"/>
+  </outputs>
+  <help>**What it does**
+
+Protein inference based on the number of identified peptides.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html
+
+@REFERENCES@
+</help>
+</tool>