--- a/FileMerger.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FileMerger.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,61 +1,103 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FileMerger" name="FileMerger" version="1.12.0">
-  <description>Merges several MS files into one file.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FileMerger</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FileMerger
+<?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: [File Handling]-->
+  <tool id="FileMerger" name="FileMerger" version="2.0.0">
+    <description>Merges several MS files into one file.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FileMerger</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FileMerger
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_annotate_file_origin:
+  -annotate_file_origin
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_rt_concat_gap:
+  -rt_concat:gap $param_rt_concat_gap
+#end if
 
--in ${param_in}
--in_type ${param_in_type}
--out ${param_out}
-${param_annotate_file_origin}
--threads \${GALAXY_SLOTS:-24} 
-${param_rt_auto}
--raw:rt_custom ${param_rt_custom}
-${param_rt_filename}
--raw:ms_level ${param_ms_level}
-${param_user_ms_level}
+##if $rep_param_rt_concat_trafo_out:
+##-rt_concat:trafo_out
+##  #for token in $rep_param_rt_concat_trafo_out:
+##    #if &quot; &quot; in str(token):
+##      &quot;$token.param_rt_concat_trafo_out&quot;
+##    #else
+##      $token.param_rt_concat_trafo_out
+##    #end if
+##  #end for
+###end if
+
+#if $param_raw_rt_auto:
+  -raw:rt_auto
+#end if
+
+#if $rep_param_raw_rt_custom:
+-raw:rt_custom
+  #for token in $rep_param_raw_rt_custom:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_raw_rt_custom&quot;
+    #else
+      $token.param_raw_rt_custom
+    #end if
+  #end for
+#end if
+#if $param_raw_rt_filename:
+  -raw:rt_filename
+#end if
+#if $param_raw_ms_level:
+  -raw:ms_level $param_raw_ms_level
+#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="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
-    <param name="param_in_type" type="select" optional="True" label="Input file type (default: determined from file extension or content)" help="(-in_type)">
-      <option value="mzData">mzData</option>
-      <option value="mzXML">mzXML</option>
-      <option value="mzML">mzML</option>
-      <option value="dta">dta</option>
-      <option value="dta2d">dta2d</option>
-      <option value="mgf">mgf</option>
-      <option value="featureXML">featureXML</option>
-      <option value="consensusXML">consensusXML</option>
-      <option value="fid">fid</option>
-      <option value="traML">traML</option>
-    </param>
-    <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." help="(-annotate_file_origin)"/>
-    <param name="param_rt_auto" type="boolean" truevalue="-raw:rt_auto true" falsevalue="-raw:rt_auto false" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto)"/>
-    <param name="param_rt_custom" type="text" size="20" value="0" label="List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file." help="(-rt_custom)"/>
-    <param name="param_rt_filename" type="boolean" truevalue="-raw:rt_filename true" falsevalue="-raw:rt_filename false" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name.#br#This option is useful for merging DTA file, which should contain the string#br#'rt' directly followed by a floating point number:#br#i.e. my_spectrum_rt2795.15.dta" help="(-rt_filename)"/>
-    <param name="param_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra." help="(-ms_level)"/>
-    <param name="param_user_ms_level" type="boolean" truevalue="-raw:user_ms_level true" falsevalue="-raw:user_ms_level false" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file" format="consensusXML">
-      <change_format>
-        <when input="param_out_type" value="mzML" format="mzML"/>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-      </change_format>
-    </data>
-  </outputs>
-  <help>**What it does**
-
-Merges several MS files into one file.
+    <inputs>
+      <param format="xml,mzml,mzxml,traml,txt,consensusxml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
+      <param help="(-gap) RT concatenation is enabled if a value &gt; 0 is set" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" name="param_rt_concat_gap" type="float" value="0.0"/>
+      <param checked="false" falsevalue="" help="(-rt_auto) " label="Assign retention times automatically (integers starting at 1)" name="param_raw_rt_auto" optional="True" truevalue="-raw:rt_auto" type="boolean"/>
+      <repeat min="0" name="rep_param_raw_rt_custom" title="param_raw_rt_custom">
+        <param help="(-rt_custom) The number of given retention times must be equal to the number of input files" label="List of custom retention times that are assigned to the files" name="param_raw_rt_custom" size="30" type="text" value="0">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param checked="false" falsevalue="" help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," name="param_raw_rt_filename" optional="True" truevalue="-raw:rt_filename" type="boolean"/>
+      <param help="(-ms_level) This option is useful for DTA files which do not contain MS level information" label="If 1 or higher, this number is assigned to spectra as the MS level" name="param_raw_ms_level" type="integer" value="0"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+      <!--<data format="trafoxml" name="param_rt_concat_trafo_out"/>-->
+    </outputs>
+    <help>Merges several MS files into one file.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
+  </tool>