--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMassAccuracy.xml	Wed Mar 01 12:24:31 2017 -0500
@@ -0,0 +1,127 @@
+<?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="IDMassAccuracy" name="IDMassAccuracy" version="2.1.0">
+  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDMassAccuracy</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDMassAccuracy
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+-id_in
+  #for token in $param_id_in:
+    $token
+  #end for
+#if $param_precursor_out:
+  -precursor_out $param_precursor_out
+#end if
+
+#if $rep_param_precursor_columns:
+-precursor_columns
+  #for token in $rep_param_precursor_columns:
+    #if " " in str(token):
+      "$token.param_precursor_columns"
+    #else
+      $token.param_precursor_columns
+    #end if
+  #end for
+#end if
+#if $param_precursor_error_ppm:
+  -precursor_error_ppm
+#end if
+#if $param_fragment_out:
+  -fragment_out $param_fragment_out
+#end if
+
+#if $rep_param_fragment_columns:
+-fragment_columns
+  #for token in $rep_param_fragment_columns:
+    #if " " in str(token):
+      "$token.param_fragment_columns"
+    #else
+      $token.param_fragment_columns
+    #end if
+  #end for
+#end if
+#if $param_fragment_error_ppm:
+  -fragment_error_ppm
+#end if
+#if $param_fragment_mass_tolerance:
+  -fragment_mass_tolerance $param_fragment_mass_tolerance
+#end if
+#if $param_separator:
+  -separator     "$param_separator"
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_number_of_bins:
+  -number_of_bins $adv_opts.param_number_of_bins
+#end if
+    #if $adv_opts.param_generate_gnuplot_scripts:
+  -generate_gnuplot_scripts
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
+      <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
+        <option value="MassDifference">MassDifference</option>
+      </param>
+    </repeat>
+    <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
+    <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
+      <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
+        <option value="MassDifference">MassDifference</option>
+      </param>
+    </repeat>
+    <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
+    <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
+    <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
+      <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
+      <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_precursor_out" format="tabular"/>
+    <data name="param_fragment_out" format="tabular"/>
+  </outputs>
+  <help>Calculates a distribution of the mass error from given mass spectra and IDs.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help>
+</tool>