<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>FidoAdapter</name>
    
    <shortDescription>
        Runs the protein inference engine Fido.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Runs the protein inference engine Fido.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html">Web Documentation for FidoAdapter</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="prob_param">Read the peptide probability from this user parameter ('UserParam') in the input file, instead of from the 'score' field, if available. (Use e.g. for search results that were processed with the TOPP tools IDPosteriorErrorProbability followed by FalseDiscoveryRate.)</option>
		<option name="separate_runs">Process multiple protein identification runs in the input separately, don't merge them. Merging results in loss of descriptive information of the single protein identification runs.</option>
		<option name="keep_zero_group">Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)</option>
		<option name="no_cleanup">Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)</option>
		<option name="all_PSMs">Consider all PSMs of each peptide, instead of only the best one</option>
		<option name="group_level">Perform inference on protein group level (instead of individual protein level). This will lead to higher probabilities for (bigger) protein groups.</option>
		<option name="accuracy">Accuracy level of start parameters. There is a trade-off between accuracy and runtime. Empty uses the default ('best').</option>
		<option name="log2_states">Binary logarithm of the max. number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18).</option>
		<option name="log2_states_precalc">Like 'log2_states', but allows to set a separate limit for the precalculation</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="protein">Protein prior probability ('gamma' parameter)</option>
		<option name="peptide">Peptide emission probability ('alpha' parameter)</option>
		<option name="spurious">Spurious peptide identification probability ('beta' parameter)</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [idXML]">Input: identification results [idXML]</inPort>
		<outPort index="0" name="out [idXML]">Output: identification results with scored/grouped proteins [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="FidoAdapter Std Output">The text sent to standard out during the execution of FidoAdapter.</view>
        <view index="1" name="FidoAdapter Error Output">The text sent to standard error during the execution of FidoAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
