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<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>MSSimulator</name>
    
    <shortDescription>
        A highly configurable simulator for mass spectrometry experiments.
    </shortDescription>
    
    <fullDescription>
        <intro><p>A highly configurable simulator for mass spectrometry experiments.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html">Web Documentation for MSSimulator</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</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="enzyme">Enzyme to use for digestion (select 'no cleavage' to skip digestion)</option>
		<option name="model">The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).</option>
		<option name="min_peptide_length">Minimum peptide length after digestion (shorter ones will be discarded)</option>
		<option name="threshold">Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.</option>
		<option name="missed_cleavages">Maximum number of missed cleavages considered. All possible resulting peptides will be created.</option>
		<option name="rt_column">Modelling of an RT or CE column</option>
		<option name="auto_scale">Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.</option>
		<option name="total_gradient_time">The duration [s] of the gradient.</option>
		<option name="sampling_rate">Time interval [s] between consecutive scans</option>
		<option name="min">Start of RT Scan Window [s]</option>
		<option name="max">End of RT Scan Window [s]</option>
		<option name="feature_stddev">Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)</option>
		<option name="affine_offset">Global offset in retention time [s] from predicted model</option>
		<option name="affine_scale">Global scaling in retention time from predicted model</option>
		<option name="distortion">Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be &gt;4.</option>
		<option name="value">Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].</option>
		<option name="variance">Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0).</option>
		<option name="value">Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.</option>
		<option name="variance">Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0).</option>
		<option name="model_file">SVM model for retention time prediction</option>
		<option name="pH">pH of buffer</option>
		<option name="alpha">Exponent Alpha used to calculate mobility</option>
		<option name="mu_eo">Electroosmotic flow</option>
		<option name="lenght_d">Length of capillary [cm] from injection site to MS</option>
		<option name="length_total">Total length of capillary [cm]</option>
		<option name="voltage">Voltage applied to capillary</option>
		<option name="dt_simulation_on">Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count</option>
		<option name="min_detect">Minimum peptide detectability accepted. Peptides with a lower score will be removed</option>
		<option name="dt_model_file">SVM model for peptide detectability prediction</option>
		<option name="ionized_residues">List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization.</option>
		<option name="charge_impurity">List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])</option>
		<option name="max_impurity_set_size">Maximal #combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'</option>
		<option name="ionization_probability">Probability for the binomial distribution of the ESI charge states</option>
		<option name="ionization_probabilities">List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)</option>
		<option name="lower_measurement_limit">Lower m/z detector limit.</option>
		<option name="upper_measurement_limit">Upper m/z detector limit.</option>
		<option name="enabled">Enable RAW signal simulation? (select 'false' if you only need feature-maps)</option>
		<option name="peak_shape">Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian.</option>
		<option name="value">Instrument resolution at 400 Th.</option>
		<option name="type">How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass.</option>
		<option name="scaling">Scale of baseline. Set to 0 to disable simulation of baseline.</option>
		<option name="shape">The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)</option>
		<option name="sampling_points">Number of raw data points per FWHM of the peak.</option>
		<option name="file">Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details.</option>
		<option name="error_stddev">Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors.</option>
		<option name="error_mean">Average systematic m/z error (Da)</option>
		<option name="scale">Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file.</option>
		<option name="scale_stddev">Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities.</option>
		<option name="rate">Poisson rate of shot noise per unit m/z. Set this to 0 to disable simulation of shot noise.</option>
		<option name="intensity-mean">Shot noise intensity mean (exponentially distributed with given mean).</option>
		<option name="mean">Mean value of white noise being added to each measured signal.</option>
		<option name="stddev">Standard deviation of white noise being added to each measured signal.</option>
		<option name="mean">Mean value of the detector noise being added to the complete measurement.</option>
		<option name="stddev">Standard deviation of the detector noise being added to the complete measurement.</option>
		<option name="status">Create Tandem-MS scans?</option>
		<option name="tandem_mode">Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity 
</option>
		<option name="svm_model_set_file">File containing the filenames of SVM Models for different charge variants</option>
		<option name="ms2_spectra_per_rt_bin">Number of allowed MS/MS spectra in a retention time bin.</option>
		<option name="min_mz_peak_distance">The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.</option>
		<option name="mz_isolation_window">All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.</option>
		<option name="exclude_overlapping_peaks">If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.</option>
		<option name="charge_filter">Charges considered for MS2 fragmentation.</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="add_single_spectra">If true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead.</option>
		<option name="add_isotopes">If set to 1 isotope peaks of the product ion peaks are added</option>
		<option name="max_isotope">Defines the maximal isotopic peak which is added, add_isotopes must be set to 1</option>
		<option name="add_metainfo">Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++</option>
		<option name="add_losses">Adds common losses to those ion expect to have them, only water and ammonia loss is considered</option>
		<option name="add_precursor_peaks">Adds peaks of the precursor to the spectrum, which happen to occur sometimes</option>
		<option name="add_abundant_immonium_ions">Add most abundant immonium ions</option>
		<option name="add_first_prefix_ion">If set to true e.g. b1 ions are added</option>
		<option name="add_y_ions">Add peaks of y-ions to the spectrum</option>
		<option name="add_b_ions">Add peaks of b-ions to the spectrum</option>
		<option name="add_a_ions">Add peaks of a-ions to the spectrum</option>
		<option name="add_c_ions">Add peaks of c-ions to the spectrum</option>
		<option name="add_x_ions">Add peaks of  x-ions to the spectrum</option>
		<option name="add_z_ions">Add peaks of z-ions to the spectrum</option>
		<option name="y_intensity">Intensity of the y-ions</option>
		<option name="b_intensity">Intensity of the b-ions</option>
		<option name="a_intensity">Intensity of the a-ions</option>
		<option name="c_intensity">Intensity of the c-ions</option>
		<option name="x_intensity">Intensity of the x-ions</option>
		<option name="z_intensity">Intensity of the z-ions</option>
		<option name="relative_loss_intensity">Intensity of loss ions, in relation to the intact ion intensity</option>
		<option name="precursor_intensity">Intensity of the precursor peak</option>
		<option name="precursor_H2O_intensity">Intensity of the H2O loss peak of the precursor</option>
		<option name="precursor_NH3_intensity">Intensity of the NH3 loss peak of the precursor</option>
		<option name="add_isotopes">If set to 1 isotope peaks of the product ion peaks are added</option>
		<option name="max_isotope">Defines the maximal isotopic peak which is added, add_isotopes must be set to 1</option>
		<option name="add_metainfo">Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++</option>
		<option name="add_first_prefix_ion">If set to true e.g. b1 ions are added</option>
		<option name="hide_y_ions">Add peaks of y-ions to the spectrum</option>
		<option name="hide_y2_ions">Add peaks of y-ions to the spectrum</option>
		<option name="hide_b_ions">Add peaks of b-ions to the spectrum</option>
		<option name="hide_b2_ions">Add peaks of b-ions to the spectrum</option>
		<option name="hide_a_ions">Add peaks of a-ions to the spectrum</option>
		<option name="hide_c_ions">Add peaks of c-ions to the spectrum</option>
		<option name="hide_x_ions">Add peaks of  x-ions to the spectrum</option>
		<option name="hide_z_ions">Add peaks of z-ions to the spectrum</option>
		<option name="hide_losses">Adds common losses to those ion expect to have them, only water and ammonia loss is considered</option>
		<option name="y_intensity">Intensity of the y-ions</option>
		<option name="b_intensity">Intensity of the b-ions</option>
		<option name="a_intensity">Intensity of the a-ions</option>
		<option name="c_intensity">Intensity of the c-ions</option>
		<option name="x_intensity">Intensity of the x-ions</option>
		<option name="z_intensity">Intensity of the z-ions</option>
		<option name="relative_loss_intensity">Intensity of loss ions, in relation to the intact ion intensity</option>
		<option name="ionization_type">Type of Ionization (MALDI or ESI)</option>
		<option name="type">Select the labeling type you want for your experiment</option>
		<option name="ICPL_fixed_rtshift">Fixed retention time shift between labeled pairs. If set to 0.0 only the retention times, computed by the RT model step are used.</option>
		<option name="label_proteins">Enables protein-labeling. (select 'false' if you only need peptide-labeling)</option>
		<option name="ICPL_light_channel_label">UniMod Id of the light channel ICPL label.</option>
		<option name="ICPL_medium_channel_label">UniMod Id of the medium channel ICPL label.</option>
		<option name="ICPL_heavy_channel_label">UniMod Id of the heavy channel ICPL label.</option>
		<option name="fixed_rtshift">Fixed retention time shift between labeled peptides. If set to 0.0 only the retention times computed by the RT model step are used.</option>
		<option name="modification_lysine">Modification of Lysine in the medium SILAC channel</option>
		<option name="modification_arginine">Modification of Arginine in the medium SILAC channel</option>
		<option name="modification_lysine">Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed.</option>
		<option name="modification_arginine">Modification of Arginine in the heavy SILAC channel. If left empty, two-channel SILAC is assumed.</option>
		<option name="iTRAQ">4plex or 8plex iTRAQ?</option>
		<option name="reporter_mass_shift">Allowed shift (uniformly distributed - left to right) in Da from the expected position (of e.g. 114.1, 115.1)</option>
		<option name="channel_active_4plex">Four-plex only: Each channel that was used in the experiment and its description (114-117) in format &lt;channel&gt;:&lt;name&gt;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;.</option>
		<option name="channel_active_8plex">Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format &lt;channel&gt;:&lt;name&gt;, e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;.</option>
		<option name="isotope_correction_values_4plex">override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' </option>
		<option name="isotope_correction_values_8plex">override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' </option>
		<option name="Y_contamination">Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling</option>
		<option name="labeling_efficiency">Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)</option>
		<option name="biological">Controls the 'biological' randomness of the generated data (e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same).</option>
		<option name="technical">Controls the 'technical' randomness of the generated data (e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same).</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [FASTA]">Input protein sequences [FASTA]</inPort>
		<outPort index="0" name="out [mzML,Inactive]">output: simulated MS raw (profile) data [mzML,Inactive]</outPort>
		<outPort index="1" name="out_pm [mzML,Inactive]">output: ground-truth picked (centroided) MS data [mzML,Inactive]</outPort>
		<outPort index="2" name="out_fm [featureXML,Inactive]">output: ground-truth features [featureXML,Inactive]</outPort>
		<outPort index="3" name="out_cm [consensusXML,Inactive]">output: ground-truth features, grouping ESI charge variants of each parent peptide [consensusXML,Inactive]</outPort>
		<outPort index="4" name="out_lcm [consensusXML,Inactive]">output: ground-truth features, grouping labeled variants [consensusXML,Inactive]</outPort>
		<outPort index="5" name="out_cntm [featureXML,Inactive]">output: ground-truth features caused by contaminants [featureXML,Inactive]</outPort>
		<outPort index="6" name="out_id [idXML,Inactive]">output: ground-truth MS2 peptide identifications [idXML,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="MSSimulator Std Output">The text sent to standard out during the execution of MSSimulator.</view>
        <view index="1" name="MSSimulator Error Output">The text sent to standard error during the execution of MSSimulator. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
