--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDScoreSwitcher.xml	Wed Mar 01 12:26:54 2017 -0500
@@ -0,0 +1,89 @@
+<?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: [Utilities]-->
+<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="2.1.0">
+  <description>Switches between different scores of peptide or protein hits in identification data</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDScoreSwitcher</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDScoreSwitcher
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_new_score:
+  -new_score     "$param_new_score"
+#end if
+#if $param_new_score_orientation:
+  -new_score_orientation
+  #if " " in str($param_new_score_orientation):
+    "$param_new_score_orientation"
+  #else
+    $param_new_score_orientation
+  #end if
+#end if
+#if $param_new_score_type:
+  -new_score_type     "$param_new_score_type"
+#end if
+#if $param_old_score:
+  -old_score     "$param_old_score"
+#end if
+#if $param_proteins:
+  -proteins
+#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_new_score" type="text" size="30" label="Name of the meta value to use as the new score" help="(-new_score) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_new_score_orientation" display="radio" type="select" optional="False" label="Orientation of the new score (are higher or lower values better?)" help="(-new_score_orientation) ">
+      <option value="lower_better">lower_better</option>
+      <option value="higher_better">higher_better</option>
+    </param>
+    <param name="param_new_score_type" type="text" size="30" label="Name to use as the type of the new score (default: same as 'new_score')" help="(-new_score_type) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_old_score" type="text" size="30" label="Name to use for the meta value storing the old score (default: old score type)" help="(-old_score) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_proteins" display="radio" type="boolean" truevalue="-proteins" falsevalue="" checked="false" optional="True" label="Apply to protein scores instead of PSM scores" help="(-proteins) "/>
+    <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>Switches between different scores of peptide or protein hits in identification data
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDScoreSwitcher.html</help>
+</tool>