--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PhosphoScoring.xml	Wed Mar 01 12:33:19 2017 -0500
@@ -0,0 +1,63 @@
+<?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: [ID Processing]-->
+<tool id="PhosphoScoring" name="PhosphoScoring" version="2.1.0">
+  <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PhosphoScoring</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PhosphoScoring
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_id:
+  -id $param_id
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_fragment_mass_tolerance:
+  -fragment_mass_tolerance $param_fragment_mass_tolerance
+#end if
+#if $param_fragment_mass_unit:
+  -fragment_mass_unit $param_fragment_mass_unit
+#end if
+#if $param_max_peptide_length:
+  -max_peptide_length $param_max_peptide_length
+#end if
+#if $param_max_num_perm:
+  -max_num_perm $param_max_num_perm
+#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="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/>
+    <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/>
+    <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/>
+    <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) ">
+      <option value="Da" selected="true">Da</option>
+      <option value="ppm">ppm</option>
+    </param>
+    <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/>
+    <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/>
+    <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>Scores potential phosphorylation sites in order to localize the most probable sites.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PhosphoScoring.html</help>
+</tool>