--- a/ProteinInference.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/ProteinInference.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,37 +1,53 @@
-<?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
+<?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="2.0.0">
+    <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
 
--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} 
+#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
+-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_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.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-min_peptides_per_protein) " label="Minimal number of peptides needed for a protein identification" min="1" name="param_min_peptides_per_protein" optional="True" type="integer" value="2"/>
+      <param checked="false" falsevalue="" help="(-treat_charge_variants_separately) " label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" name="param_treat_charge_variants_separately" optional="True" truevalue="-treat_charge_variants_separately" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-treat_modification_variants_separately) " label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" name="param_treat_modification_variants_separately" optional="True" truevalue="-treat_modification_variants_separately" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </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
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html</help>
+  </tool>