<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="ProteinInference" docurl="http://www.openms.de/documentation/TOPP_ProteinInference.html" category="Identification" >
<description><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.]]></description>
<manual><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.]]></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="ProteinInference" description="Protein inference based on an aggregation of the scores of the identified peptides.">
    <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;ProteinInference&apos;">
      <ITEMLIST name="in" type="input-file" description="input file(s)" required="true" advanced="false" supported_formats="*.idXML">
      </ITEMLIST>
      <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.idXML" />
      <ITEM name="merge_runs" value="no" type="string" description="If your idXML contains multiple runs, merge them beforehand?" required="false" advanced="false" restrictions="no,all" />
      <ITEM name="annotate_indist_groups" value="true" type="string" description="If you want to annotate indistinguishable protein groups, either for reporting or for group based quant. later. Only works with a single ID run in the file." 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="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="Merging" description="">
        <ITEM name="annotate_origin" value="true" type="string" description="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from." required="false" advanced="false" restrictions="true,false" />
        <ITEM name="allow_disagreeing_settings" value="false" type="bool" description="Force merging of disagreeing runs. Use at your own risk." required="false" advanced="false" />
      </NODE>
      <NODE name="Algorithm" description="">
        <ITEM name="min_peptides_per_protein" value="1" type="int" description="Minimal number of peptides needed for a protein identification. If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept." required="false" advanced="false" restrictions="0:" />
        <ITEM name="score_aggregation_method" value="maximum" type="string" description="How to aggregate scores of peptides matching to the same protein?" required="false" advanced="false" restrictions="maximum,product,sum" />
        <ITEM name="treat_charge_variants_separately" value="true" type="string" description="If this is set, different charge variants of the same peptide sequence count as individual evidences." required="false" advanced="false" />
        <ITEM name="treat_modification_variants_separately" value="true" type="string" description="If this is set, different modification variants of the same peptide sequence count as individual evidences." required="false" advanced="false" />
        <ITEM name="use_shared_peptides" value="true" type="string" description="If this is set, shared peptides are used as evidences." required="false" advanced="false" />
        <ITEM name="skip_count_annotation" value="false" type="string" description="If this is true, peptide counts won&apos;t be annotated at the proteins." required="false" advanced="false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>