<?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

##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 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</help>
  </tool>