--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInference.xml	Wed Mar 01 12:46:36 2017 -0500
@@ -0,0 +1,52 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Identification]-->
+<tool id="ProteinInference" name="ProteinInference" version="2.1.0">
+  <description>Protein inference based on the number of identified peptides.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ProteinInference</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ProteinInference
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_min_peptides_per_protein:
+  -min_peptides_per_protein $param_min_peptides_per_protein
+#end if
+#if $param_treat_charge_variants_separately:
+  -treat_charge_variants_separately
+#end if
+#if $param_treat_modification_variants_separately:
+  -treat_modification_variants_separately
+#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="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" display="radio" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" 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" display="radio" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" 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) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+  </outputs>
+  <help>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</help>
+</tool>