<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="TargetedFileConverter" docurl="http://www.openms.de/documentation/UTILS_TargetedFileConverter.html" category="Targeted Experiments" >
<description><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.]]></description>
<manual><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.]]></manual>
<citations>
  <citation doi="10.1038/nmeth.3959" url="" />
</citations>
<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="TargetedFileConverter" description="Converts different transition files for targeted proteomics / metabolomics analysis.">
    <ITEM name="version" value="2.6.0-pre-exported-20201001" 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;TargetedFileConverter&apos;">
      <ITEM name="in" value="" type="input-file" description="Input file to convert.#br# See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file." required="true" advanced="false" supported_formats="*.tsv,*.mrm,*.pqp,*.TraML" />
      <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" required="false" advanced="false" restrictions="tsv,mrm,pqp,TraML" />
      <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.tsv,*.pqp,*.TraML" />
      <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content#br#Note: not all conversion paths work or make sense." required="false" advanced="false" restrictions="tsv,pqp,TraML" />
      <ITEM name="legacy_traml_id" value="false" type="bool" description="PQP to TraML: Should legacy TraML IDs be used?" required="false" advanced="true" />
      <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="bool" description="Disables progress logging to command line" required="false" advanced="true" />
      <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
      <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
      <NODE name="algorithm" description="Algorithm parameters section">
        <ITEM name="retentionTimeInterpretation" value="iRT" type="string" description="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" required="false" advanced="true" restrictions="iRT,seconds,minutes" />
        <ITEM name="override_group_label_check" value="false" type="bool" description="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing." required="false" advanced="true" />
        <ITEM name="force_invalid_mods" value="false" type="bool" description="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" required="false" advanced="true" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>