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<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="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="greedy_group_resolution">Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities. Also adds the resolved ambiguity groups to output.</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>
