<?xml version="1.0" encoding="UTF-8"?>
<tool version="2.0.0" name="FileMerger" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html" category="File Handling" >
<description><![CDATA[Merges several MS files into one file.]]></description>
<manual><![CDATA[Merges several MS files into one file.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="FileMerger" description="Merges several MS files into one file.">
    <ITEM name="version" value="2.0.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FileMerger&apos;">
      <ITEMLIST name="in" type="input-file" description="Input files separated by blank" required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML">
      </ITEMLIST>
      <ITEM name="in_type" value="" type="string" description="Input file type (default: determined from file extension or content)" required="false" advanced="false" restrictions="mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML" />
      <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
      <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
      <NODE name="raw" description="Flags for non-featureXML input/output">
        <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" />
        <ITEMLIST name="rt_custom" type="double" description="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." required="false" advanced="false">
        </ITEMLIST>
        <ITEM name="rt_filename" value="false" type="string" description="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#&apos;rt&apos; directly followed by a floating point number:#br#i.e. my_spectrum_rt2795.15.dta" required="false" advanced="false" restrictions="true,false" />
        <ITEM name="ms_level" value="2" type="int" description="This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra." required="false" advanced="false" />
        <ITEM name="user_ms_level" value="false" type="string" description="If this flag is set, the MS level given above is used" required="false" advanced="false" restrictions="true,false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
