<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="FileConverter" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html" category="File Handling" >
<description><![CDATA[Converts between different MS file formats.]]></description>
<manual><![CDATA[Converts between different MS file formats.]]></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="FileConverter" description="Converts between different MS file formats.">
    <ITEM name="version" value="2.1.0" 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;FileConverter&apos;">
      <ITEM name="in" value="" type="input-file" description="Input file to convert." required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta" />
      <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content#br#" required="false" advanced="false" restrictions="mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta" />
      <ITEM name="UID_postprocessing" value="ensure" type="string" description="unique ID post-processing for output data.#br#&apos;none&apos; keeps current IDs even if invalid.#br#&apos;ensure&apos; keeps current IDs but reassigns invalid ones.#br#&apos;reassign&apos; assigns new unique IDs." required="false" advanced="false" restrictions="none,ensure,reassign" />
      <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv" />
      <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." required="false" advanced="false" restrictions="mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv" />
      <ITEM name="TIC_DTA2D" value="false" type="string" description="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="MGF_compact" value="false" type="string" description="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="write_mzML_index" value="false" type="string" description="Add an index to the file when writing mzML files (default: no index)" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="process_lowmemory" value="false" type="string" description="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." required="false" advanced="true" 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>
  </NODE>
</PARAMETERS>
</tool>
