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<?xml version="1.0" encoding="ISO-8859-1"?>
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<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">
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<NODE name="info" description="">
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<ITEM name="version" value="1.9.0" type="string" description="" />
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<ITEM name="num_vertices" value="7" type="int" description="" />
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<ITEM name="num_edges" value="6" type="int" description="" />
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<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:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> <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;"></p></body></html>]]>" type="string" description="" />
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<NODE name="vertices" description="">
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<NODE name="0" description="">
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<ITEM name="recycle_output" value="false" type="string" description="" />
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<ITEM name="toppas_type" value="input file list" type="string" description="" />
13
<ITEMLIST name="file_names" type="string" description="">
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<LISTITEM value="../BSA/BSA1.mzML"/>
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<LISTITEM value="../BSA/BSA2.mzML"/>
16
<LISTITEM value="../BSA/BSA3.mzML"/>
18
<ITEM name="x_pos" value="-140" type="float" description="" />
19
<ITEM name="y_pos" value="-160" type="float" description="" />
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<NODE name="1" description="">
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<ITEM name="recycle_output" value="false" type="string" description="" />
23
<ITEM name="toppas_type" value="tool" type="string" description="" />
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<ITEM name="tool_name" value="FeatureFinderCentroided" type="string" description="" />
25
<ITEM name="tool_type" value="" type="string" description="" />
26
<ITEM name="x_pos" value="-140" type="float" description="" />
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<ITEM name="y_pos" value="-40" type="float" description="" />
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<NODE name="parameters" description="Instance '1' section for 'FeatureFinderCentroided'">
29
<ITEM name="in" value="" type="string" description="input file" tags="input file,required" restrictions="*.mzML" />
30
<ITEM name="out" value="" type="string" description="output file" tags="output file,required" restrictions="*.featureXML" />
31
<ITEM name="seeds" value="" type="string" description="User specified seed list" tags="input file" restrictions="*.featureXML" />
32
<ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" />
33
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
34
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
35
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
36
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
37
<NODE name="algorithm" description="Algorithm section">
38
<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" />
39
<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)">
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<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:" />
42
<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).">
43
<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:" />
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<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:" />
45
<ITEM name="max_missing" value="1" type="int" description="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" restrictions="0:" />
46
<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:" />
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<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).">
49
<ITEM name="charge_low" value="2" type="int" description="Lowest charge to search for." restrictions="1:" />
50
<ITEM name="charge_high" value="3" type="int" description="Highest charge to search for." restrictions="1:" />
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<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:" />
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<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" />
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<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" />
54
<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" />
55
<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" />
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<NODE name="seed" description="Settings that determine which peaks are considered a seed">
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<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" />
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<NODE name="fit" description="Settings for the model fitting">
61
<ITEM name="epsilon_abs" value="0.0001" type="float" description="Absolute epsilon used for convergence of the fit." tags="advanced" restrictions="0:" />
62
<ITEM name="epsilon_rel" value="0.0001" type="float" description="Relative epsilon used for convergence of the fit." tags="advanced" restrictions="0:" />
63
<ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." tags="advanced" restrictions="1:" />
65
<NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)">
66
<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" />
67
<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" />
68
<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" />
69
<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" />
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<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:" />
71
<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" />
72
<ITEM name="max_intersection" value="0.35" type="float" description="Maximum allowed intersection of features." tags="advanced" restrictions="0:1" />
73
<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" />
75
<NODE name="user-seed" description="Settings for user-specified seeds.">
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<ITEM name="rt_tolerance" value="5" type="float" description="Allowed RT deviation of seeds from the user-specified seed position." restrictions="0:" />
77
<ITEM name="mz_tolerance" value="1.1" type="float" description="Allowed m/z deviation of seeds from the user-specified seed position." restrictions="0:" />
78
<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" />
80
<NODE name="debug" description="">
81
<ITEM name="pseudo_rt_shift" value="500" type="float" description="Pseudo RT shift used when ." tags="advanced" restrictions="1:" />
86
<NODE name="2" description="">
87
<ITEM name="recycle_output" value="false" type="string" description="" />
88
<ITEM name="toppas_type" value="input file list" type="string" description="" />
89
<ITEMLIST name="file_names" type="string" description="">
90
<LISTITEM value="../BSA/BSA1_OMSSA.idXML"/>
91
<LISTITEM value="../BSA/BSA2_OMSSA.idXML"/>
92
<LISTITEM value="../BSA/BSA3_OMSSA.idXML"/>
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<ITEM name="x_pos" value="60" type="float" description="" />
95
<ITEM name="y_pos" value="-160" type="float" description="" />
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<NODE name="3" description="">
98
<ITEM name="recycle_output" value="false" type="string" description="" />
99
<ITEM name="toppas_type" value="tool" type="string" description="" />
100
<ITEM name="tool_name" value="IDMapper" type="string" description="" />
101
<ITEM name="tool_type" value="" type="string" description="" />
102
<ITEM name="x_pos" value="60" type="float" description="" />
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<ITEM name="y_pos" value="-40" type="float" description="" />
104
<NODE name="parameters" description="Instance '1' section for 'IDMapper'">
105
<ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" restrictions="*.idXML" />
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<ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" />
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<ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" restrictions="*.featureXML,*.consensusXML" />
108
<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:" />
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<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:" />
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<ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." restrictions="ppm,Da" />
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<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" />
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<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" />
113
<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" />
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<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" />
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<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" />
116
<ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" />
117
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
118
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
119
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
120
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
123
<NODE name="5" description="">
124
<ITEM name="recycle_output" value="false" type="string" description="" />
125
<ITEM name="toppas_type" value="tool" type="string" description="" />
126
<ITEM name="tool_name" value="FeatureLinkerUnlabeled" type="string" description="" />
127
<ITEM name="tool_type" value="" type="string" description="" />
128
<ITEM name="x_pos" value="60" type="float" description="" />
129
<ITEM name="y_pos" value="260" type="float" description="" />
130
<NODE name="parameters" description="Instance '1' section for 'FeatureLinkerUnlabeled'">
131
<ITEMLIST name="in" type="string" description="input files separated by blanks" tags="input file,required" restrictions="*.featureXML,*.consensusXML">
133
<ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.consensusXML" />
134
<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" />
135
<ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" />
136
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
137
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
138
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
139
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
140
<NODE name="algorithm" description="Algorithm parameters section">
141
<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:" />
142
<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" />
143
<ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" />
144
<NODE name="distance_RT" description="Distance component based on RT differences">
145
<ITEM name="max_difference" value="100" type="float" description="Maximum allowed difference in RT" restrictions="0:" />
146
<ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" />
147
<ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" />
149
<NODE name="distance_MZ" description="Distance component based on m/z differences">
150
<ITEM name="max_difference" value="0.3" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" />
151
<ITEM name="unit" value="Da" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" />
152
<ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" />
153
<ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" />
155
<NODE name="distance_intensity" description="Distance component based on differences in relative intensity">
156
<ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" />
157
<ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" />
162
<NODE name="6" description="">
163
<ITEM name="recycle_output" value="false" type="string" description="" />
164
<ITEM name="toppas_type" value="output file list" type="string" description="" />
165
<ITEM name="x_pos" value="-120" type="float" description="" />
166
<ITEM name="y_pos" value="260" type="float" description="" />
168
<NODE name="4" description="">
169
<ITEM name="recycle_output" value="false" type="string" description="" />
170
<ITEM name="toppas_type" value="merger" type="string" description="" />
171
<ITEM name="x_pos" value="60" type="float" description="" />
172
<ITEM name="y_pos" value="100" type="float" description="" />
173
<ITEM name="round_based" value="false" type="string" description="" />
176
<NODE name="edges" description="">
177
<NODE name="0" description="">
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<NODE name="source/target" description="">
179
<ITEM name="" value="1/3" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="out" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="in" type="string" description="" />
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<NODE name="1" description="">
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<NODE name="source/target" description="">
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<ITEM name="" value="2/3" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="__no_name__" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="id" type="string" description="" />
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<NODE name="2" description="">
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<NODE name="source/target" description="">
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<ITEM name="" value="0/1" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="__no_name__" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="in" type="string" description="" />
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<NODE name="3" description="">
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<NODE name="source/target" description="">
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<ITEM name="" value="5/6" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="out" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="__no_name__" type="string" description="" />
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<NODE name="4" description="">
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<NODE name="source/target" description="">
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<ITEM name="" value="3/4" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="out" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="__no_name__" type="string" description="" />
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<NODE name="5" description="">
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<NODE name="source/target" description="">
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<ITEM name="" value="4/5" type="string" description="" />
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<NODE name="source_out_param" description="">
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<ITEM name="" value="__no_name__" type="string" description="" />
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<NODE name="target_in_param" description="">
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<ITEM name="" value="in" type="string" description="" />
added
removed
source/TEST/TOPP/INIUpdater_1_noupdate.toppas
