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    <name>IDPosteriorErrorProbability</name>
    
    <shortDescription>
        Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html">Web Documentation for IDPosteriorErrorProbability</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="split_charge">The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed.</option>
		<option name="top_hits_only">If set only the top hits of every PeptideIdentification will be used</option>
		<option name="fdr_for_targets_smaller">Only used, when top_hits_only set. Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run.</option>
		<option name="ignore_bad_data">If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through.</option>
		<option name="prob_correct">If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications.</option>
		<option name="log">Name of log file (created only when specified)</option>
		<option name="debug">Sets the debug level</option>
		<option name="threads">Sets the number of threads allowed to be used by the TOPP tool</option>
		<option name="no_progress">Disables progress logging to command line</option>
		<option name="force">Overwrite tool specific checks.</option>
		<option name="test">Enables the test mode (needed for internal use only)</option>
		<option name="number_of_bins">Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized</option>
		<option name="incorrectly_assigned">for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used.</option>
		<option name="max_nr_iterations">Bounds the number of iterations for the EM algorithm when convergence is slow.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [idXML]">input file  [idXML]</inPort>
		<outPort index="0" name="out [idXML]">output file  [idXML]</outPort>
		<outPort index="1" name="out_plot [txt,Inactive]">txt file (if gnuplot is available, a corresponding PDF will be created as well.) [txt,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="IDPosteriorErrorProbability Std Output">The text sent to standard out during the execution of IDPosteriorErrorProbability.</view>
        <view index="1" name="IDPosteriorErrorProbability Error Output">The text sent to standard error during the execution of IDPosteriorErrorProbability. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
