Created
January 17, 2017 08:55
-
-
Save lars20070/c5719b437e2291f1ac4d7c3600a4459e to your computer and use it in GitHub Desktop.
OpenMS workflow, peptide feature detection, Sciex TripleTOF 6600, 7/01/2017
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="7" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="6" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> </p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">[1] mzML profile input data</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">[2] baseline removal (in order to apply universal intensity cutoff in the next step)</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">[3] intensity cutoff &gt;120</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">[4] smoothing of the spectra in m/z direction</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">[5] feature detection</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">[6] mzML profile data after preprocessing</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">[7] detected peptide features (featureXML)</span></p></body></html>]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| <LISTITEM value="../../../Lars/2015/20150709_FixedRatio_TripleTOF_Joern/data/SILAC_1_2000_3000.mzML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-360" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="280" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="preprocessed" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FeatureFinderMultiplex" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="520" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="LC-MS dataset in centroid or profile mode" required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="output-file" description="Optional output file containing the individual peptide features in 'out'." required="false" advanced="true" supported_formats="*.featureXML" /> | |
| <ITEM name="out_mzq" value="" type="output-file" description="Optional output file of MzQuantML." required="false" advanced="true" supported_formats="*.mzq" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="labels" value="" type="string" description="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10] ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC#br#[Dimethyl0][Dimethyl6] ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL" required="false" advanced="false" /> | |
| <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." required="false" advanced="false" /> | |
| <ITEM name="isotopes_per_peptide" value="3:5" type="string" description="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " required="false" advanced="true" /> | |
| <ITEM name="rt_typical" value="50" type="double" description="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="rt_min" value="10" type="double" description="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="10" type="double" description="m/z tolerance for search of peak patterns." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz_unit" value="ppm" type="string" description="Unit of the 'mz_tolerance' parameter." required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="intensity_cutoff" value="10" type="double" description="Lower bound for the intensity of isotopic peaks." required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="peptide_similarity" value="0.9" type="double" description="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity" value="0.8" type="double" description="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." required="false" advanced="false" restrictions="-1:1" /> | |
| <ITEM name="averagine_similarity_scaling" value="0.75" type="double" description="Let x denote this scaling factor, and p the averagine similarity parameter. For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)" required="false" advanced="true" restrictions="0:1" /> | |
| <ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="knock_out" value="false" type="string" description="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="averagine_type" value="peptide" type="string" description="The type of averagine to use, currently RNA, DNA or peptide" required="false" advanced="true" restrictions="peptide,RNA,DNA" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'algorithm:labels'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="double" description="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="double" description="Label:2H(4) | H(-4) 2H(4) | unimod #481" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="double" description="Label:13C(6) | C(-6) 13C(6) | unimod #188" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="double" description="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Leu3" value="3.01883" type="double" description="Label:2H(3) | H(-3) 2H(3) | unimod #262" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl0" value="28.0313" type="double" description="Dimethyl | H(4) C(2) | unimod #36" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl4" value="32.056407" type="double" description="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl6" value="34.063117" type="double" description="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="Dimethyl8" value="36.07567" type="double" description="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL0" value="105.021464" type="double" description="ICPL | H(3) C(6) N O | unimod #365" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL4" value="109.046571" type="double" description="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL6" value="111.041593" type="double" description="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="ICPL10" value="115.0667" type="double" description="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" required="false" advanced="true" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="720" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="BaselineFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-120" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input raw data file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="output raw data file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="struc_elem_length" value="0.3" type="double" description="Length of the structuring element (should be wider than maximal peak width - see documentation)." required="false" advanced="false" /> | |
| <ITEM name="struc_elem_unit" value="Thomson" type="string" description="Unit of 'struc_elem_length' parameter." required="false" advanced="false" restrictions="Thomson,DataPoints" /> | |
| <ITEM name="method" value="tophat" type="string" description="The name of the morphological filter to be applied. If you are unsure, use the default." required="false" advanced="false" restrictions="identity,erosion,dilation,opening,closing,gradient,tophat,bothat,erosion_simple,dilation_simple" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="80" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract" required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract (applies to ALL ms levels!)" required="false" advanced="false" /> | |
| <ITEM name="int" value="120:1000000000" type="string" description="Intensity range to extract" required="false" advanced="false" /> | |
| <ITEM name="sort" value="false" type="string" description="Sorts the output according to RT and m/z." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="peak_options" description="Peak data options"> | |
| <ITEM name="sn" value="0" type="double" description="Write peaks with S/N > 'sn' values only" required="false" advanced="false" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="pc_mz_range" value=":" type="string" description="MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag." required="false" advanced="false" /> | |
| <ITEMLIST name="pc_mz_list" type="double" description="List of m/z values. If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract" required="false" advanced="false"> | |
| <LISTITEM value="1"/> | |
| <LISTITEM value="2"/> | |
| <LISTITEM value="3"/> | |
| </ITEMLIST> | |
| <ITEM name="sort_peaks" value="false" type="string" description="Sorts the peaks according to m/z" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="mz_precision" value="64" type="string" description="Store base64 encoded m/z data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="int_precision" value="32" type="string" description="Store base64 encoded intensity data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="indexed_file" value="false" type="string" description="Whether to add an index to the file when writing" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="numpress" description="Numpress compression for peak data"> | |
| <ITEM name="masstime" value="none" type="string" description="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="masstime_error" value="0.0001" type="double" description="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| <ITEM name="intensity" value="none" type="string" description="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="intensity_error" value="0.0001" type="double" description="Maximal allowable error in intensity dimension (set to 0.5 for pic)" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="spectra" description="Remove spectra or select spectra (removing all others) with certain properties"> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="remove_activation" value="" type="string" description="Remove MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="remove_collision_energy" value=":" type="string" description="Remove MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="remove_isolation_window_width" value=":" type="string" description="Remove MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Retain MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation" /> | |
| <ITEM name="select_collision_energy" value=":" type="string" description="Select MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_isolation_window_width" value=":" type="string" description="Select MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_polarity" value="" type="string" description="Retain MSn scans with a certain scan polarity" required="false" advanced="false" restrictions="unknown,positive,negative" /> | |
| </NODE> | |
| <NODE name="feature" description="Feature data options"> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Consensus feature data options"> | |
| <ITEMLIST name="map" type="int" description="Maps to be extracted from a consensus" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="blackorwhitelist" description="Black or white listing of of MS2 spectra by consensus features"> | |
| <ITEM name="blacklist" value="true" type="string" description="True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept" required="false" advanced="false" restrictions="false,true" /> | |
| <ITEM name="file" value="" type="input-file" description="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.#br#If consensus:blackorwhitelist:maps is specified, only these will be used.#br#" required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEMLIST name="maps" type="int" description="Maps used for black/white list filtering" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="rt" value="60" type="double" description="Retention tolerance [s] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.01" type="double" description="m/z tolerance [Th] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="use_ppm_tolerance" value="false" type="string" description="If ppm tolerance should be used. Otherwise Da are used." required="false" advanced="false" restrictions="false,true" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="f_and_c" description="Feature & Consensus data options"> | |
| <ITEM name="charge" value=":" type="string" description="Charge range to extract" required="false" advanced="false" /> | |
| <ITEM name="size" value=":" type="string" description="Size range to extract" required="false" advanced="false" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="id" description="ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="Remove features with id clashes (different sequences mapped to one feature)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="keep_best_score_id" value="false" type="string" description="in case of multiple peptide identifications, keep only the id with best score" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="Remove features with annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="Remove features without annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="Remove unassigned peptide identifications" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="blacklist" value="" type="input-file" description="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'id:rt' and 'id:mz' options.#br#This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rt" value="0.1" type="double" description="Retention tolerance [s] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.001" type="double" description="m/z tolerance [Th] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="blacklist_imperfect" value="false" type="string" description="Allow for mismatching precursor positions (see 'id:blacklist')" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="algorithm" description="S/N algorithm section"> | |
| <NODE name="SignalToNoise" description=""> | |
| <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" /> | |
| <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" /> | |
| <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" /> | |
| <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> | |
| <ITEM name="write_log_messages" value="true" type="string" description="Write out log messages in case of sparse windows or median in rightmost histogram bin" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="NoiseFilterSGolay" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="280" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input raw data file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="output raw data file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="processOption" value="inmemory" type="string" description="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" required="false" advanced="true" restrictions="inmemory,lowmemory" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="frame_length" value="15" type="int" description="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." required="false" advanced="false" /> | |
| <ITEM name="polynomial_order" value="4" type="int" description="Order or the polynomial that is fitted." required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/6" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out_features" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/2" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/1" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/3" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/4" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/5" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment