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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="1.9.0" type="string" description="" /> | |
| <ITEM name="num_vertices" value="25" type="int" description="" /> | |
| <ITEM name="num_edges" value="30" type="int" description="" /> | |
| <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;">SILAC analysis pipeline for Thermo Orbi XL data with identification from TPP reporting proteins present as light and heavy, light only as well as heavy only</p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></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;">input [1]: mzML in profile mode</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;">input [2]: pep.xml from TPP ID pipeline</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;">input [3]: prot.xml from TPP ID pipeline</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></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;">output [25]: abundances for light only proteins</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;">output [23]: abundances for heavy only proteins</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;">output [9]: abundances for proteins present as light and heavy</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></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;">Output of [10] and [4] contain singlets and doublets respectively. Output of [15] contains singlets that are not part of the doublets. Output of [22] and [18] conatain singlets with light and heavy annotations respectively.</span></p> | |
| <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></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;">Lars Nilse l.nilse@dunelm.org.uk</span></p></body></html>]]>" type="string" description="" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| <LISTITEM value="data/yanliu_O1112_001.mzML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-240" type="float" description="" /> | |
| <ITEM name="y_pos" value="-280" type="float" description="" /> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| <LISTITEM value="data/yanliu_O1112_001_pepXML.idXML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="180" type="float" description="" /> | |
| <ITEM name="y_pos" value="-280" type="float" description="" /> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" /> | |
| <ITEMLIST name="file_names" type="string" description=""> | |
| <LISTITEM value="data/interact.prot.xml"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="380" type="float" description="" /> | |
| <ITEM name="y_pos" value="-280" type="float" description="" /> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="SILACAnalyzer" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-100" type="float" description="" /> | |
| <ITEM name="y_pos" value="-100" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" 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." tags="output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_clusters" value="" type="string" description="Optional debug output containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="string" description="Optional output file containing the individual peptide features in 'out'." tags="advanced,output file" restrictions="*.featureXML" /> | |
| <ITEM name="out_filters" value="" type="string" description="Optional output file containing all points that passed the filters as txt. Suitable as input for 'in_filters' to perform clustering without preceding filtering process." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="in_filters" value="" type="string" description="Optional input file containing all points that passed the filters as txt. Use output from 'out_filters' to perform clustering only." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_debug" value="" type="string" description="Filename base for debug output." tags="advanced" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="4" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="allow_missing_peaks" value="false" type="string" description="Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="rt_threshold" value="40" type="float" 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.)" restrictions="0:" /> | |
| <ITEM name="rt_min" value="0" type="float" description="Lower bound for the retention time [s]." restrictions="0:" /> | |
| <ITEM name="intensity_cutoff" value="5000" type="float" description="Lower bound for the intensity of isotopic peaks in a SILAC pattern." restrictions="0:" /> | |
| <ITEM name="intensity_correlation" value="0.7" type="float" description="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." restrictions="0:1" /> | |
| <ITEM name="model_deviation" value="3" type="float" description="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'sample'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="float" description="Arg6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="float" description="Arg10 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="float" description="Lys4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="float" description="Lys6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="float" description="Lys8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL4" value="4.025107" type="float" description="mass difference between isotope-coded protein labels ICPL 4 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL6" value="6.020129" type="float" description="mass difference between isotope-coded protein labels ICPL 6 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL10" value="10.045236" type="float" description="mass difference between isotope-coded protein labels ICPL 10 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl4" value="4.0202" type="float" description="Methyl4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl8" value="8.0202" type="float" description="Methyl8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl12" value="12.0202" type="float" description="Methyl12 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl16" value="16.0202" type="float" description="Methyl16 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl24" value="24.0202" type="float" description="Methyl24 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl32" value="32.0202" type="float" description="Methyl32 mass shift" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="sample" description="Parameters describing the sample and its labels."> | |
| <ITEM name="labels" value="[Lys8,Arg10]" type="string" description="Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see 'advanced parameters', section 'labels'. If left empty the tool identifies singlets, i.e. acts as peptide feature finder." /> | |
| <ITEM name="charge" value="1:4" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." /> | |
| <ITEM name="missed_cleavages" value="2" type="int" description="Maximum number of missed cleavages." restrictions="0:" /> | |
| <ITEM name="peaks_per_peptide" value="3:8" type="string" description="Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDFileConverter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="180" type="float" description="" /> | |
| <ITEM name="y_pos" value="300" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#xml: Single mascot XML file.#br#idXML: Single idXML file.#br#" tags="input file,required" /> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.idXML,*.mzid,*.pepXML,*.FASTA" /> | |
| <ITEM name="out_type" value="idXML" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="idXML,mzid,pepXML,FASTA" /> | |
| <ITEM name="mz_file" value="" type="string" description="MS data file from which the pepXML was generated. Used to look up retention times (some pepXMLs contain only scan numbers) and/or to define what parts to extract (some pepXMLs contain results from multiple experiments)." /> | |
| <ITEM name="ignore_proteins_per_peptide" value="false" type="string" description="Workaround to deal with .out files that contain e.g. "+1" in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="mz_name" value="" type="string" description="Experiment filename/path to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." /> | |
| <ITEM name="use_precursor_data" value="false" type="string" description="Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDFileConverter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="380" type="float" description="" /> | |
| <ITEM name="y_pos" value="880" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#xml: Single mascot XML file.#br#idXML: Single idXML file.#br#" tags="input file,required" /> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.idXML,*.mzid,*.pepXML,*.FASTA" /> | |
| <ITEM name="out_type" value="idXML" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="idXML,mzid,pepXML,FASTA" /> | |
| <ITEM name="mz_file" value="" type="string" description="MS data file from which the pepXML was generated. Used to look up retention times (some pepXMLs contain only scan numbers) and/or to define what parts to extract (some pepXMLs contain results from multiple experiments)." /> | |
| <ITEM name="ignore_proteins_per_peptide" value="false" type="string" description="Workaround to deal with .out files that contain e.g. "+1" in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="mz_name" value="" type="string" description="Experiment filename/path to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." /> | |
| <ITEM name="use_precursor_data" value="false" type="string" description="Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" restrictions="*.idXML" /> | |
| <ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="rt_tolerance" value="20" type="float" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="30" type="float" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." restrictions="ppm,Da" /> | |
| <ITEM name="mz_reference" value="precursor" type="string" description="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'use_centroid_mz' to avoid false-positive matches.)" restrictions="precursor,peptide" /> | |
| <ITEM name="ignore_charge" value="true" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." restrictions="true,false" /> | |
| <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." restrictions="true,false" /> | |
| <ITEM name="use_centroid_mz" value="false" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" restrictions="true,false" /> | |
| <ITEM name="use_subelements" value="true" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="380" type="float" description="" /> | |
| <ITEM name="y_pos" value="1420" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" /> | |
| <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" /> | |
| <ITEM name="id_out" value="" type="string" description="Output file for peptide and protein abundances (annotated idXML) - suitable for export to mzTab.#br#Either 'out', 'peptide_out', or 'id_out' are required. They can be used together." tags="output file" restrictions="*.idXML" /> | |
| <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" restrictions="0:" /> | |
| <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,mean,sum" /> | |
| <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" restrictions="true,false" /> | |
| <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" /> | |
| <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" restrictions="none,double,escape" /> | |
| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="380" type="float" description="" /> | |
| <ITEM name="y_pos" value="1620" type="float" description="" /> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="SILACAnalyzer" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-380" type="float" description="" /> | |
| <ITEM name="y_pos" value="-100" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" 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." tags="output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_clusters" value="" type="string" description="Optional debug output containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_features" value="" type="string" description="Optional output file containing the individual peptide features in 'out'." tags="advanced,output file" restrictions="*.featureXML" /> | |
| <ITEM name="out_filters" value="" type="string" description="Optional output file containing all points that passed the filters as txt. Suitable as input for 'in_filters' to perform clustering without preceding filtering process." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="in_filters" value="" type="string" description="Optional input file containing all points that passed the filters as txt. Use output from 'out_filters' to perform clustering only." tags="advanced,output file" restrictions="*.consensusXML" /> | |
| <ITEM name="out_debug" value="" type="string" description="Filename base for debug output." tags="advanced" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Parameters for the algorithm."> | |
| <ITEM name="allow_missing_peaks" value="false" type="string" description="Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="rt_threshold" value="40" type="float" 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.)" restrictions="0:" /> | |
| <ITEM name="rt_min" value="0" type="float" description="Lower bound for the retention time [s]." restrictions="0:" /> | |
| <ITEM name="intensity_cutoff" value="5000" type="float" description="Lower bound for the intensity of isotopic peaks in a SILAC pattern." restrictions="0:" /> | |
| <ITEM name="intensity_correlation" value="0.7" type="float" description="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." restrictions="0:1" /> | |
| <ITEM name="model_deviation" value="3" type="float" description="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="labels" description="Isotopic labels that can be specified in section 'sample'."> | |
| <ITEM name="Arg6" value="6.0201290268" type="float" description="Arg6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Arg10" value="10.0082686" type="float" description="Arg10 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys4" value="4.0251069836" type="float" description="Lys4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys6" value="6.0201290268" type="float" description="Lys6 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Lys8" value="8.0141988132" type="float" description="Lys8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL4" value="4.025107" type="float" description="mass difference between isotope-coded protein labels ICPL 4 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL6" value="6.020129" type="float" description="mass difference between isotope-coded protein labels ICPL 6 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="dICPL10" value="10.045236" type="float" description="mass difference between isotope-coded protein labels ICPL 10 and ICPL 0" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl4" value="4.0202" type="float" description="Methyl4 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl8" value="8.0202" type="float" description="Methyl8 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl12" value="12.0202" type="float" description="Methyl12 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl16" value="16.0202" type="float" description="Methyl16 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl24" value="24.0202" type="float" description="Methyl24 mass shift" tags="advanced" restrictions="0:" /> | |
| <ITEM name="Methyl32" value="32.0202" type="float" description="Methyl32 mass shift" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="sample" description="Parameters describing the sample and its labels."> | |
| <ITEM name="labels" value="" type="string" description="Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see 'advanced parameters', section 'labels'. If left empty the tool identifies singlets, i.e. acts as peptide feature finder." /> | |
| <ITEM name="charge" value="1:4" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." /> | |
| <ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages." restrictions="0:" /> | |
| <ITEM name="peaks_per_peptide" value="3:8" type="string" description="Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-180" type="float" description="" /> | |
| <ITEM name="y_pos" value="60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value=":" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| <LISTITEM value="0"/> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="0" type="float" description="" /> | |
| <ITEM name="y_pos" value="60" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value=":" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| <LISTITEM value="1"/> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureLinkerUnlabeledQT" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-380" type="float" description="" /> | |
| <ITEM name="y_pos" value="300" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="input files separated by blanks" tags="input file,required" restrictions="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.consensusXML" /> | |
| <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="30" type="float" description="Maximum allowed difference in RT" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="30" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" /> | |
| <ITEM name="x_pos" value="-380" type="float" description="" /> | |
| <ITEM name="y_pos" value="140" type="float" description="" /> | |
| <ITEM name="round_based" value="true" type="string" description="" /> | |
| </NODE> | |
| <NODE name="24" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="-140" type="float" description="" /> | |
| <ITEM name="y_pos" value="1620" type="float" description="" /> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-160" type="float" description="" /> | |
| <ITEM name="y_pos" value="300" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value="1:1" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| <LISTITEM value="2"/> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="15" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="IDMapper" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-80" type="float" description="" /> | |
| <ITEM name="y_pos" value="520" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" restrictions="*.idXML" /> | |
| <ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="rt_tolerance" value="20" type="float" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="30" type="float" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." restrictions="0:" /> | |
| <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." restrictions="ppm,Da" /> | |
| <ITEM name="mz_reference" value="precursor" type="string" description="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'use_centroid_mz' to avoid false-positive matches.)" restrictions="precursor,peptide" /> | |
| <ITEM name="ignore_charge" value="true" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." restrictions="true,false" /> | |
| <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." restrictions="true,false" /> | |
| <ITEM name="use_centroid_mz" value="false" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" restrictions="true,false" /> | |
| <ITEM name="use_subelements" value="true" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="16" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-80" type="float" description="" /> | |
| <ITEM name="y_pos" value="700" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value=":" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="true" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="true" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="17" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="880" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value=":" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| <LISTITEM value="(Label:13C(6)15N(4))"/> | |
| <LISTITEM value="(Label:13C(6)15N(2))"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="20" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureLinkerUnlabeledQT" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-140" type="float" description="" /> | |
| <ITEM name="y_pos" value="1040" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="string" description="input files separated by blanks" tags="input file,required" restrictions="*.featureXML,*.consensusXML"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.consensusXML" /> | |
| <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." restrictions="true,false" /> | |
| <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" /> | |
| <NODE name="distance_RT" description="Distance component based on RT differences"> | |
| <ITEM name="max_difference" value="30" type="float" description="Maximum allowed difference in RT" restrictions="0:" /> | |
| <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_MZ" description="Distance component based on m/z differences"> | |
| <ITEM name="max_difference" value="30" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="ppm" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" /> | |
| <ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> | |
| <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" /> | |
| <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="18" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" /> | |
| <ITEM name="x_pos" value="-140" type="float" description="" /> | |
| <ITEM name="y_pos" value="880" type="float" description="" /> | |
| <ITEM name="round_based" value="true" type="string" description="" /> | |
| </NODE> | |
| <NODE name="21" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-140" type="float" description="" /> | |
| <ITEM name="y_pos" value="1220" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="input file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract" /> | |
| <ITEM name="rt" value=":" type="string" description="retention time range to extract" /> | |
| <ITEM name="int" value=":" type="string" description="intensity range to extract" /> | |
| <ITEM name="sort" value="false" type="string" description="sorts the output according to RT and m/z." restrictions="true,false" /> | |
| <ITEM name="sn" value="0" type="float" description="write peaks with S/N > 'sn' values only" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract"> | |
| <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." restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans." restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file." restrictions="true,false" /> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode#br#" restrictions="Unknown,MassSpectrum,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#br#" 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_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" restrictions="Unknown,MassSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion" /> | |
| <ITEM name="select_activation" value="" type="string" description="Select MSn scans where any of its precursors features a certain activation method#br#" 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="charge" value=":" type="string" description="charge range to extract" /> | |
| <ITEM name="size" value="1:1" type="string" description="size range to extract" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple, 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!"> | |
| </ITEMLIST> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" /> | |
| <ITEMLIST name="map" type="int" description="maps to be extracted from a consensus"> | |
| <LISTITEM value="1"/> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="AND connective of map selection instead of OR." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="id" description="id section"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="remove features with id clashes (different sequences mapped to one feature)" tags="advanced" 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" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="remove features with annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="remove features without annotations" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="remove unassigned peptide identifications" 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." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" 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)" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="22" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" /> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="1620" type="float" description="" /> | |
| </NODE> | |
| <NODE name="23" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="-140" type="float" description="" /> | |
| <ITEM name="y_pos" value="1420" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" /> | |
| <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" /> | |
| <ITEM name="id_out" value="" type="string" description="Output file for peptide and protein abundances (annotated idXML) - suitable for export to mzTab.#br#Either 'out', 'peptide_out', or 'id_out' are required. They can be used together." tags="output file" restrictions="*.idXML" /> | |
| <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" restrictions="0:" /> | |
| <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,mean,sum" /> | |
| <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" restrictions="true,false" /> | |
| <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" /> | |
| <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" restrictions="none,double,escape" /> | |
| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="19" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" /> | |
| <ITEM name="tool_type" value="" type="string" description="" /> | |
| <ITEM name="x_pos" value="120" type="float" description="" /> | |
| <ITEM name="y_pos" value="1420" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" /> | |
| <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" restrictions="*.idXML" /> | |
| <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" /> | |
| <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" /> | |
| <ITEM name="id_out" value="" type="string" description="Output file for peptide and protein abundances (annotated idXML) - suitable for export to mzTab.#br#Either 'out', 'peptide_out', or 'id_out' are required. They can be used together." tags="output file" restrictions="*.idXML" /> | |
| <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" restrictions="0:" /> | |
| <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,mean,sum" /> | |
| <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" restrictions="true,false" /> | |
| <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" /> | |
| <NODE name="consensus" description="Additional options for consensus maps"> | |
| <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" restrictions="true,false" /> | |
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| </NODE> | |
| <NODE name="format" description="Output formatting options"> | |
| <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the 'tab' character is used" /> | |
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| <ITEM name="replacement" value="_" type="string" description="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" /> | |
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| </PARAMETERS> |
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from old website's workflow section:
SILAC analysis pipeline for Thermo Orbi XL data with identification from TPP reporting proteins present as light and heavy, light only as well as heavy only
input [1]: mzML in profile mode
input [2]: pep.xml from TPP ID pipeline
input [3]: prot.xml from TPP ID pipeline
output [25]: abundances for light only proteins
output [23]: abundances for heavy only proteins
output [9]: abundances for proteins present as light and heavy
Output of [10] and [4] contain singlets and doublets respectively. Output of [15] contains singlets that are not part of the doublets. Output of [22] and [18] conatain singlets with light and heavy annotations respectively.
Lars Nilse l.nilse@dunelm.org.uk