<?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

-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}
</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.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html

@REFERENCES@
</help>
</tool>