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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>MetaProSIP</name>
    
    <shortDescription>
        Performs proteinSIP on peptide features for elemental flux analysis.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Performs proteinSIP on peptide features for elemental flux analysis.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html">Web Documentation for MetaProSIP</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="mz_tolerance_ppm">Tolerance in ppm</option>
		<option name="rt_tolerance_s">Rolerance window around feature rt for XIC extraction</option>
		<option name="intensity_threshold">Intensity threshold to collect peaks in the MS1 spectrum.</option>
		<option name="correlation_threshold">Correlation threshold for reporting a RIA</option>
		<option name="xic_threshold">Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak. If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present.</option>
		<option name="decomposition_threshold">Minimum R&sup2; of decomposition that must be achieved for a peptide to be reported.</option>
		<option name="weight_merge_window">Decomposition coefficients within +- this rate window will be combined</option>
		<option name="min_correlation_distance_to_averagine">Minimum difference in correlation between incorporation pattern and averagine pattern. Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1</option>
		<option name="pattern_15N_TIC_threshold">The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.</option>
		<option name="pattern_13C_TIC_threshold">The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.</option>
		<option name="heatmap_bins">Number of RIA bins for heat map generation.</option>
		<option name="plot_extension">Extension used for plots (png|svg|pdf).</option>
		<option name="qc_output_directory">Output directory for the quality report</option>
		<option name="use_15N">Use 15N instead of 13C</option>
		<option name="use_unassigned_ids">Include identifications not assigned to a feature in pattern detection.</option>
		<option name="use_averagine_ids">Use averagine peptides as model to perform pattern detection on unidentified peptides.</option>
		<option name="report_natural_peptides">Whether purely natural peptides are reported in the quality report.</option>
		<option name="filter_monoisotopic">Try to filter out mono-isotopic patterns to improve detection of low RIA patterns</option>
		<option name="cluster">Perform grouping</option>
		<option name="observed_peak_fraction">Fraction of observed/expected peaks.</option>
		<option name="min_consecutive_isotopes">Minimum number of consecutive isotopic intensities needed.</option>
		<option name="score_plot_yaxis_min">The minimum value of the score axis. Values smaller than zero usually only make sense if the observed peak fraction is set to 0.</option>
		<option name="collect_method">How RIAs are collected.</option>
		<option name="lowRIA_correlation_threshold">Correlation threshold for reporting low RIA patterns. Disable and take correlation_threshold value for negative values.</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>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in_mzML [mzML]">Centroided MS1 data [mzML]</inPort>
		<inPort index="1" name="in_fasta [fasta]">Protein sequence database [fasta]</inPort>
		<inPort index="2" name="in_featureXML [featureXML]">Feature data annotated with identifications (IDMapper) [featureXML]</inPort>
		<outPort index="0" name="out_csv [csv]">Column separated file with feature fitting result. [csv]</outPort>
		<outPort index="1" name="out_peptide_centric_csv [csv]">Column separated file with peptide centric result. [csv]</outPort>
 </ports>
    <views>
        <view index="0" name="MetaProSIP Std Output">The text sent to standard out during the execution of MetaProSIP.</view>
        <view index="1" name="MetaProSIP Error Output">The text sent to standard error during the execution of MetaProSIP. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
