--- a/FeatureFinderMetabo.xml	Mon Feb 12 08:46:55 2018 -0500
+++ b/FeatureFinderMetabo.xml	Wed May 15 05:46:43 2019 -0400
@@ -1,7 +1,7 @@
 <?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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
-<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.2.0">
+<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.3.0">
   <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>FeatureFinderMetabo
+  <command detect_errors="aggressive"><![CDATA[FeatureFinderMetabo
 
 #if $param_in:
   -in $param_in
@@ -18,6 +18,9 @@
 #if $param_out:
   -out $param_out
 #end if
+#if $param_out_chrom:
+  -out_chrom $param_out_chrom
+#end if
 #if $param_algorithm_common_noise_threshold_int:
   -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
 #end if
@@ -85,7 +88,7 @@
   #end if
 #end if
 #if $param_algorithm_ffm_mz_scoring_13C:
-  -algorithm:ffm:mz_scoring_13C
+  -algorithm:ffm:mz_scoring_13C true
 #end if
 #if $param_algorithm_ffm_report_convex_hulls:
   -algorithm:ffm:report_convex_hulls
@@ -141,7 +144,7 @@
   #end if
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
     <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
@@ -176,6 +179,12 @@
       <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
       <option value="peptides">peptides</option>
       <option value="none">none</option>
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
     </param>
     <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
     <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
@@ -203,9 +212,10 @@
   </inputs>
   <outputs>
     <data name="param_out" format="featurexml"/>
+    <data name="param_out_chrom" format="mzml"/>
   </outputs>
   <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help>
 </tool>