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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>InclusionExclusionListCreator</name>
    
    <shortDescription>
        Creates inclusion and/or exclusion lists.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Creates inclusion and/or exclusion lists.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html">Web Documentation for InclusionExclusionListCreator</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="inclusion_charges">List containing the charge states to be considered for the inclusion list compounds, space separated.</option>
		<option name="inclusion_strategy">strategy to be used for selection</option>
		<option name="exclusion_charges">List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated.</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="missed_cleavages">Number of missed cleavages used for protein digestion.
</option>
		<option name="unit">Create lists with units as seconds instead of minutes</option>
		<option name="use_relative">Use relative RT window, which depends on RT of precursor.</option>
		<option name="window_relative">[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X].</option>
		<option name="window_absolute">[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X].</option>
		<option name="mz_tol">Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'.</option>
		<option name="mz_tol_unit">Unit of 'mz_tol'</option>
		<option name="rt_tol">Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds].</option>
		<option name="ms2_spectra_per_rt_bin">Number of allowed MS/MS spectra in a retention time bin.</option>
		<option name="exclude_overlapping_peaks">If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.</option>
		<option name="use_dynamic_exclusion">If true dynamic exclusion is applied.</option>
		<option name="exclusion_time">The time (in seconds) a feature is excluded.</option>
		<option name="max_list_size">The maximal number of precursors in the inclusion list.</option>
		<option name="min_rt">Minimal rt in seconds.</option>
		<option name="max_rt">Maximal rt in seconds.</option>
		<option name="rt_step_size">rt step size in seconds.</option>
		<option name="rt_window_size">rt window size in seconds.</option>
		<option name="min_protein_id_probability">Minimal protein probability for a protein to be considered identified.</option>
		<option name="min_pt_weight">Minimal pt weight of a precursor</option>
		<option name="min_mz">Minimal mz to be considered in protein based LP formulation.</option>
		<option name="max_mz">Minimal mz to be considered in protein based LP formulation.</option>
		<option name="use_peptide_rule">Use peptide rule instead of minimal protein id probability</option>
		<option name="min_peptide_ids">If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id</option>
		<option name="min_peptide_probability">If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified</option>
		<option name="no_intensity_normalization">Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1.</option>
		<option name="max_number_precursors_per_feature">The maximal number of precursors per feature.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="include [featureXML,fasta]">Inclusion list input file in FASTA or featureXML format. [featureXML,fasta,opt.]</inPort>
		<inPort index="1" name="exclude [featureXML,idXML,fasta]">Exclusion list input file in featureXML, idXML or FASTA format. [featureXML,idXML,fasta,opt.]</inPort>
		<inPort index="2" name="rt_model [txt]">RTModel file used for the rt prediction of peptides in FASTA files. [txt,opt.]</inPort>
		<inPort index="3" name="pt_model [txt]">PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP). [txt,opt.]</inPort>
		<inPort index="4" name="raw_data [mzML]">File containing the raw data (only needed for FeatureBased_LP). [mzML,opt.]</inPort>
		<outPort index="0" name="out [csv]">Output file (tab delimited csv file). [csv]</outPort>
 </ports>
    <views>
        <view index="0" name="InclusionExclusionListCreator Std Output">The text sent to standard out during the execution of InclusionExclusionListCreator.</view>
        <view index="1" name="InclusionExclusionListCreator Error Output">The text sent to standard error during the execution of InclusionExclusionListCreator. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
