--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaboliteSpectralMatcher.xml	Wed Mar 01 12:16:51 2017 -0500
@@ -0,0 +1,69 @@
+<?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="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.1.0">
+  <description>Find potential HMDB ids within the given mass error window.</description>
+  <macros>
+    <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MetaboliteSpectralMatcher
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_algorithm_prec_mass_error_value:
+  -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
+#end if
+#if $param_algorithm_frag_mass_error_value:
+  -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
+#end if
+#if $param_algorithm_mass_error_unit:
+  -algorithm:mass_error_unit $param_algorithm_mass_error_unit
+#end if
+#if $param_algorithm_report_mode:
+  -algorithm:report_mode $param_algorithm_report_mode
+#end if
+#if $param_algorithm_ionization_mode:
+  -algorithm:ionization_mode $param_algorithm_ionization_mode
+#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="mzML file" help="(-in) "/>
+    <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
+    <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
+    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
+      <option value="ppm" selected="true">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_algorithm_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
+      <option value="top3" selected="true">top3</option>
+      <option value="best">best</option>
+    </param>
+    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
+      <option value="positive" selected="true">positive</option>
+      <option value="negative">negative</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_out" format="tabular"/>
+  </outputs>
+  <help>Find potential HMDB ids within the given mass error window.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help>
+</tool>