--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinResolver.xml	Wed Mar 01 12:38:04 2017 -0500
@@ -0,0 +1,124 @@
+<?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: [Quantitation]-->
+<tool id="ProteinResolver" name="ProteinResolver" version="2.1.0">
+  <description>protein inference</description>
+  <macros>
+    <token name="@EXECUTABLE@">ProteinResolver</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ProteinResolver
+
+#if $param_fasta:
+  -fasta $param_fasta
+#end if
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_in_path:
+  -in_path     "$param_in_path"
+#end if
+#if $param_design:
+  -design $param_design
+#end if
+#if $param_protein_groups:
+  -protein_groups $param_protein_groups
+#end if
+#if $param_peptide_table:
+  -peptide_table $param_peptide_table
+#end if
+#if $param_protein_table:
+  -protein_table $param_protein_table
+#end if
+#if $param_additional_info:
+  -additional_info $param_additional_info
+#end if
+#if $param_resolver_missed_cleavages:
+  -resolver:missed_cleavages $param_resolver_missed_cleavages
+#end if
+#if $param_resolver_min_length:
+  -resolver:min_length $param_resolver_min_length
+#end if
+#if $param_resolver_enzyme:
+  -resolver:enzyme $param_resolver_enzyme
+#end if
+#if $param_designer_experiment:
+  -designer:experiment     "$param_designer_experiment"
+#end if
+#if $param_designer_file:
+  -designer:file     "$param_designer_file"
+#end if
+#if $param_designer_separator:
+  -designer:separator $param_designer_separator
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_fasta" type="data" format="fasta" optional="False" label="Input database file" help="(-fasta) "/>
+    <param name="param_in" type="data" format="consensusxml,idxml" multiple="true" optional="True" size="30" label="Input file(s) holding experimental data" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_in_path" type="text" size="30" label="Path to idXMLs or consensusXMLs files" help="(-in_path) Ignored if 'in' is given">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_design" type="data" format="txt" optional="True" label="Text file containing the experimental design" help="(-design) See documentation for specific format requirements"/>
+    <param name="param_resolver_missed_cleavages" type="integer" min="0" optional="True" value="2" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
+    <param name="param_resolver_min_length" type="integer" min="1" optional="True" value="6" label="Minimum length of peptide" help="(-min_length) "/>
+    <param name="param_resolver_enzyme" display="radio" type="select" optional="False" value="Trypsin" label="Digestion enzyme" help="(-enzyme) ">
+      <option value="Trypsin" selected="true">Trypsin</option>
+    </param>
+    <param name="param_designer_experiment" type="text" size="30" value="ExperimentalSetting" label="Identifier for the experimental design" help="(-experiment) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_designer_file" type="text" size="30" value="File" label="Identifier for the file name" help="(-file) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_designer_separator" display="radio" type="select" optional="False" value="tab" label="Separator, which should be used to split a row into columns" help="(-separator) ">
+      <option value="tab" selected="true">tab</option>
+      <option value="semi-colon">semi-colon</option>
+      <option value="comma">comma</option>
+      <option value="whitespace">whitespace</option>
+    </param>
+    <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_protein_groups" format="tabular"/>
+    <data name="param_peptide_table" format="tabular"/>
+    <data name="param_protein_table" format="tabular"/>
+    <data name="param_additional_info" format="tabular"/>
+  </outputs>
+  <help>protein inference
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help>
+</tool>