<?xml version='1.0' encoding='UTF-8'?>
<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="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_raw_rt_auto:
  -raw:rt_auto
#end if

#if $rep_param_raw_rt_custom:
-raw:rt_custom
  #for token in $rep_param_raw_rt_custom:
    #if " " in str(token):
      "$token.param_raw_rt_custom"
    #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 $param_raw_user_ms_level:
  -raw:user_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="mgf,mzml,mzxml,traml,featurexml,consensusxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin" falsevalue="" 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_raw_rt_auto" 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="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 given input file">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_raw_rt_filename" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name" help="(-rt_filename) &lt;br&gt;This option is useful for merging DTA file, which should contain the string &lt;br&gt;'rt' directly followed by a floating point number: &lt;br&gt;i.e. my_spectrum_rt2795.15.dta"/>
    <param name="param_raw_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information" help="(-ms_level) The given level is assigned to the spectra"/>
    <param name="param_raw_user_ms_level" type="boolean" truevalue="-raw:user_ms_level" falsevalue="" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level) "/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>**What it does**

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>
  <expand macro="references"/>
</tool>