--- a/FileMerger.xml	Thu Jan 11 17:45:16 2018 -0500
+++ b/FileMerger.xml	Mon Feb 12 13:09:49 2018 -0500
@@ -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: [File Handling]-->
-<tool id="FileMerger" name="FileMerger" version="2.2.0">
+<tool id="FileMerger" name="FileMerger" version="2.3.0">
   <description>Merges several MS files into one file.</description>
   <macros>
     <token name="@EXECUTABLE@">FileMerger</token>
@@ -26,6 +26,16 @@
   -rt_concat:gap $param_rt_concat_gap
 #end if
 
+#if $rep_param_rt_concat_trafo_out:
+-rt_concat:trafo_out
+  #for token in $rep_param_rt_concat_trafo_out:
+    #if " " in str(token):
+      "$token.param_rt_concat_trafo_out"
+    #else
+      $token.param_rt_concat_trafo_out
+    #end if
+  #end for
+#end if
 #if $param_raw_rt_auto:
   -raw:rt_auto
 #end if
@@ -53,7 +63,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
+    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -65,7 +75,7 @@
     <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
     <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
     <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
-      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
+      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
         <sanitizer>
           <valid initial="string.printable">
             <remove value="'"/>
@@ -81,7 +91,8 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="mzml"/>
+    <data name="param_out" format="featurexml"/>
+    <data name="param_rt_concat_trafo_out" format="trafoxml"/>
   </outputs>
   <help>Merges several MS files into one file.