<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="DatabaseSuitability" docurl="" category="" >
<description><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.]]></description>
<manual><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.]]></manual>
<citations>
  <citation doi="10.1038/nmeth.3959" url="" />
  <citation doi="10.1074/mcp.TIR119.001752" 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="DatabaseSuitability" description="Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.">
    <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;DatabaseSuitability&apos;">
      <ITEM name="in_id" value="" type="input-file" description="Input idXML file from peptide search with combined database with added de novo peptide. PeptideIndexer is needed, FDR is forbidden." required="true" advanced="false" supported_formats="*.idXML" />
      <ITEM name="in_spec" value="" type="input-file" description="Input MzML file used for the peptide identification" required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="in_novo" value="" type="input-file" description="Input idXML file containing de novo peptides (unfiltered)" required="true" advanced="false" supported_formats="*.idXML" />
      <ITEM name="out" value="" type="output-file" description="Optional tsv output containing database suitability information as well as spectral quality." required="false" advanced="false" supported_formats="*.tsv" />
      <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="Parameter section for the suitability calculation algorithm">
        <ITEM name="no_rerank" value="false" type="bool" description="Use this flag if you want to disable re-ranking. Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality." required="false" advanced="false" />
        <ITEM name="reranking_cutoff_percentile" value="0.01" type="double" description="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM. The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top." required="false" advanced="false" restrictions="0.0:1.0" />
        <ITEM name="FDR" value="0.01" type="double" description="Filter peptide hits based on this q-value. (e.g., 0.05 = 5 % FDR)" required="false" advanced="false" restrictions="0.0:1.0" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>