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June 8, 2016 13:10
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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="7" type="int" description="" /> | |
| <ITEM name="num_edges" value="6" 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;"> <span style=" color:#000000;">This workflow performs a simple quantification, assuming you have already performed an ID.</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;">Node #1 expects mzML files. Node #2 finds the features in these maps and passes on featureXML files.</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;">Corresponding peptide identifications in idXML format are expected in input node #3. They are mapped to the corresponding featureXML files by the IDMapper.</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;">The Collect node waits for all processing rounds to finish, then runs FeatureLinkerUnlabeled once, with a list of all annotated featureXML files as input, which creates a single consensusXML output file.</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=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-320" type="float" description="" /> | |
| <ITEM name="y_pos" value="-40" type="float" description="" /> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="FeatureFinderCentroided" 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="-40" type="float" description="" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="string" description="input file" tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.featureXML" /> | |
| <ITEM name="seeds" value="" type="string" description="User-specified seed list. This feature is not supported by all algorithms!" tags="input file" restrictions="*.featureXML" /> | |
| <ITEM name="log" value="TOPP.log" 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 section"> | |
| <ITEM name="debug" value="false" type="string" description="When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode)." restrictions="true,false" /> | |
| <NODE name="intensity" description="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)"> | |
| <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." restrictions="1:" /> | |
| </NODE> | |
| <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)."> | |
| <ITEM name="mz_tolerance" value="0.005" type="float" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="min_spectra" value="7" type="int" description="Number of spectra that have to show a similar peak mass in a mass trace." restrictions="1:" /> | |
| <ITEM name="max_missing" value="1" type="int" description="Number of spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" restrictions="0:" /> | |
| <ITEM name="slope_bound" value="0.5" type="float" description="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." restrictions="0:" /> | |
| </NODE> | |
| <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotoipic pattern (between 0 and 1)."> | |
| <ITEM name="charge_low" value="2" type="int" description="Lowest charge to search for." restrictions="1:" /> | |
| <ITEM name="charge_high" value="3" type="int" description="Highest charge to search for." restrictions="1:" /> | |
| <ITEM name="mz_tolerance" value="0.005" type="float" description="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" /> | |
| <ITEM name="intensity_percentage" value="10" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="intensity_percentage_optional" value="0.1" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="optional_fit_improvement" value="2" type="float" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak." tags="advanced" restrictions="0:100" /> | |
| <ITEM name="mass_window_width" value="25" type="float" description="Window width in Dalton for precalculation of estimated isotope distribtions." tags="advanced" restrictions="1:200" /> | |
| </NODE> | |
| <NODE name="seed" description="Settings that determine which peaks are considered a seed"> | |
| <ITEM name="min_score" value="0.8" type="float" description="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="fit" description="Settings for the model fitting"> | |
| <ITEM name="epsilon_abs" value="0.0001" type="float" description="Absolute epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="epsilon_rel" value="0.0001" type="float" description="Relative epsilon used for convergence of the fit." tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)"> | |
| <ITEM name="min_score" value="0.7" type="float" description="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." restrictions="0:1" /> | |
| <ITEM name="min_isotope_fit" value="0.8" type="float" description="Minimum isotope fit of the feature before model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_trace_score" value="0.5" type="float" description="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="min_rt_span" value="0.333" type="float" description="Minimum RT span in relation to extended area that has to remain after model fitting." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="max_rt_span" value="2.5" type="float" description="Maximum RT span in relation to extended area that the model is allowed to have." tags="advanced" restrictions="0.5:" /> | |
| <ITEM name="rt_shape" value="symmetric" type="string" description="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." tags="advanced" restrictions="symmetric,asymmetric" /> | |
| <ITEM name="max_intersection" value="0.35" type="float" description="Maximum allowed intersection of features." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="reported_mz" value="monoisotopic" type="string" description="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." restrictions="maximum,average,monoisotopic" /> | |
| </NODE> | |
| <NODE name="user-seed" description="Settings for user-specified seeds."> | |
| <ITEM name="rt_tolerance" value="5" type="float" description="Allowed RT deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="mz_tolerance" value="1.1" type="float" description="Allowed m/z deviation of seeds from the user-specified seed position." restrictions="0:" /> | |
| <ITEM name="min_score" value="0.5" type="float" description="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." restrictions="0:1" /> | |
| </NODE> | |
| <NODE name="debug" description=""> | |
| <ITEM name="pseudo_rt_shift" value="500" type="float" description="Pseudo RT shift used when ." tags="advanced" restrictions="1:" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </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=""> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-320" type="float" description="" /> | |
| <ITEM name="y_pos" value="120" 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="IDMapper" 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="120" 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="5" 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="20" 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="false" 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="false" 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="TOPP.log" 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="FeatureLinkerUnlabeled" 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="120" 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="TOPP.log" 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="second_nearest_gap" value="2" type="float" description="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself" restrictions="1:" /> | |
| <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="100" 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="0.3" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" /> | |
| <ITEM name="unit" value="Da" 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="6" 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="180" type="float" description="" /> | |
| <ITEM name="y_pos" value="-40" type="float" description="" /> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="merger" type="string" description="" /> | |
| <ITEM name="x_pos" value="20" type="float" description="" /> | |
| <ITEM name="y_pos" value="120" type="float" description="" /> | |
| <ITEM name="round_based" value="false" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/3" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/3" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="id" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/1" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/6" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/4" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/5" type="string" description="" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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from old website's workflow section:
�This workflow performs a simple quantification, assuming you have already performed an ID.
Node #1 expects mzML files. Node #2 finds the features in these maps and passes on featureXML files.
Corresponding peptide identifications in idXML format are expected in input node #3. They are mapped to the corresponding featureXML files by the IDMapper.
The Collect node waits for all processing rounds to finish, then runs FeatureLinkerUnlabeled once, with a list of all annotated featureXML files as input, which creates a single consensusXML output file.