Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
view test-data/examples/TOPPAS/BSA_Quantitation.toppas @ 18:6daaa75ccb99 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
| author | galaxyp |
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| date | Sun, 13 Dec 2020 15:03:50 +0000 |
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<?xml version="1.0" encoding="ISO-8859-1"?> <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <NODE name="info" description=""> <ITEM name="version" value="1.11.0" type="string" description="" required="false" advanced="false" /> <ITEM name="num_vertices" value="7" type="int" description="" required="false" advanced="false" /> <ITEM name="num_edges" value="6" type="int" description="" required="false" advanced="false" /> <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">This workflow performs a simple quantification of three label-free bovine serum albumine (BSA) runs.</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;"></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 contains three mzML files. Node #2 finds the features on these maps and passes on three 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;"></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 (obtained using OMSSA in advance) are mapped to each of these 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;"></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 three rounds to finish, then runs FeatureLinkerUnlabeled once, with a list of all three annotated featureXML files as input, which creates a single consensusXML output file.</span></p></body></html>]]>" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="vertices" description=""> <NODE name="0" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> <LISTITEM value="../BSA/BSA1.mzML"/> <LISTITEM value="../BSA/BSA2.mzML"/> <LISTITEM value="../BSA/BSA3.mzML"/> </ITEMLIST> <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="1" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_name" value="FeatureFinderCentroided" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEM name="in" value="" type="input-file" description="input file" required="true" advanced="false" supported_formats="*.mzML" /> <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.featureXML" /> <ITEM name="seeds" value="" type="input-file" description="User specified seed list" required="false" advanced="false" supported_formats="*.featureXML" /> <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> <NODE name="algorithm" description="Algorithm 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)." required="false" advanced="false" 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." required="false" advanced="false" 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="double" 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!" required="false" advanced="false" 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." required="false" advanced="false" restrictions="1:" /> <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'!" required="false" advanced="false" restrictions="0:" /> <ITEM name="slope_bound" value="0.5" type="double" 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." required="false" advanced="false" restrictions="0:" /> </NODE> <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)."> <ITEM name="charge_low" value="2" type="int" description="Lowest charge to search for." required="false" advanced="false" restrictions="1:" /> <ITEM name="charge_high" value="3" type="int" description="Highest charge to search for." required="false" advanced="false" restrictions="1:" /> <ITEM name="mz_tolerance" value="0.005" type="double" 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!" required="false" advanced="false" restrictions="0:" /> <ITEM name="intensity_percentage" value="10" type="double" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." required="false" advanced="true" restrictions="0:100" /> <ITEM name="intensity_percentage_optional" value="0.1" type="double" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." required="false" advanced="true" restrictions="0:100" /> <ITEM name="optional_fit_improvement" value="2" type="double" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak." required="false" advanced="true" restrictions="0:100" /> <ITEM name="mass_window_width" value="25" type="double" description="Window width in Dalton for precalculation of estimated isotope distributions." required="false" advanced="true" restrictions="1:200" /> <ITEM name="abundance_12C" value="98.93" type="double" description="Rel. abundance of the light carbon. Modify if labeled." required="false" advanced="true" restrictions="0:100" /> <ITEM name="abundance_14N" value="99.632" type="double" description="Rel. abundance of the light nitrogen. Modify if labeled." required="false" advanced="true" restrictions="0:100" /> </NODE> <NODE name="seed" description="Settings that determine which peaks are considered a seed"> <ITEM name="min_score" value="0.8" type="double" 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." required="false" advanced="false" restrictions="0:1" /> </NODE> <NODE name="fit" description="Settings for the model fitting"> <ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." required="false" advanced="true" restrictions="1:" /> </NODE> <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)"> <ITEM name="min_score" value="0.7" type="double" 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." required="false" advanced="false" restrictions="0:1" /> <ITEM name="min_isotope_fit" value="0.8" type="double" description="Minimum isotope fit of the feature before model fitting." required="false" advanced="true" restrictions="0:1" /> <ITEM name="min_trace_score" value="0.5" type="double" 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." required="false" advanced="true" restrictions="0:1" /> <ITEM name="min_rt_span" value="0.333" type="double" description="Minimum RT span in relation to extended area that has to remain after model fitting." required="false" advanced="true" restrictions="0:1" /> <ITEM name="max_rt_span" value="2.5" type="double" description="Maximum RT span in relation to extended area that the model is allowed to have." required="false" advanced="true" 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." required="false" advanced="true" restrictions="symmetric,asymmetric" /> <ITEM name="max_intersection" value="0.35" type="double" description="Maximum allowed intersection of features." required="false" advanced="true" 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." required="false" advanced="false" restrictions="maximum,average,monoisotopic" /> </NODE> <NODE name="user-seed" description="Settings for user-specified seeds."> <ITEM name="rt_tolerance" value="5" type="double" description="Allowed RT deviation of seeds from the user-specified seed position." required="false" advanced="false" restrictions="0:" /> <ITEM name="mz_tolerance" value="1.1" type="double" description="Allowed m/z deviation of seeds from the user-specified seed position." required="false" advanced="false" restrictions="0:" /> <ITEM name="min_score" value="0.5" type="double" description="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." required="false" advanced="false" restrictions="0:1" /> </NODE> <NODE name="debug" description=""> <ITEM name="pseudo_rt_shift" value="500" type="double" description="Pseudo RT shift used when ." required="false" advanced="true" restrictions="1:" /> </NODE> </NODE> </NODE> </NODE> <NODE name="2" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> <LISTITEM value="../BSA/BSA1_OMSSA.idXML"/> <LISTITEM value="../BSA/BSA2_OMSSA.idXML"/> <LISTITEM value="../BSA/BSA3_OMSSA.idXML"/> </ITEMLIST> <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="3" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_name" value="IDMapper" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEM name="id" value="" type="input-file" description="Protein/peptide identifications file" required="true" advanced="false" supported_formats="*.idXML" /> <ITEM name="in" value="" type="input-file" description="Feature map/consensus map file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> <ITEM name="out" value="" type="output-file" description="Output file (the format depends on the input file format)." required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML,*.mzq" /> <ITEM name="rt_tolerance" value="5" type="double" 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." required="false" advanced="false" restrictions="0:" /> <ITEM name="mz_tolerance" value="20" type="double" 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." required="false" advanced="false" restrictions="0:" /> <ITEM name="mz_measure" value="ppm" type="string" description="Unit of 'mz_tolerance'." required="false" advanced="false" 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 'feature:use_centroid_mz' to avoid false-positive matches.)" required="false" advanced="false" 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." required="false" advanced="false" restrictions="true,false" /> <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> <NODE name="feature" description="Additional options for featureXML input"> <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." required="false" advanced="false" 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.)" required="false" advanced="false" restrictions="true,false" /> </NODE> <NODE name="consensus" description="Additional options for consensusXML input"> <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." required="false" advanced="false" restrictions="true,false" /> </NODE> </NODE> </NODE> <NODE name="5" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_name" value="FeatureLinkerUnlabeled" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="180" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEMLIST name="in" type="input-file" description="input files separated by blanks" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML"> </ITEMLIST> <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.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." required="false" advanced="false" restrictions="true,false" /> <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> <NODE name="algorithm" description="Algorithm parameters section"> <ITEM name="second_nearest_gap" value="2" type="double" description="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." required="false" advanced="false" 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)." required="false" advanced="false" restrictions="true,false" /> <ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" required="false" advanced="false" restrictions="true,false" /> <NODE name="distance_RT" description="Distance component based on RT differences"> <ITEM name="max_difference" value="100" type="double" description="Maximum allowed difference in RT in seconds" required="false" advanced="false" restrictions="0:" /> <ITEM name="exponent" value="1" type="double" description="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> <ITEM name="weight" value="1" type="double" description="RT distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> </NODE> <NODE name="distance_MZ" description="Distance component based on m/z differences"> <ITEM name="max_difference" value="0.3" type="double" description="Maximum allowed difference in m/z (unit defined by 'unit')" required="false" advanced="false" restrictions="0:" /> <ITEM name="unit" value="Da" type="string" description="Unit of the 'max_difference' parameter" required="false" advanced="false" restrictions="Da,ppm" /> <ITEM name="exponent" value="2" type="double" description="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> <ITEM name="weight" value="1" type="double" description="m/z distances are weighted by this factor" required="false" advanced="true" restrictions="0:" /> </NODE> <NODE name="distance_intensity" description="Distance component based on differences in relative intensity"> <ITEM name="exponent" value="1" type="double" description="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" required="false" advanced="true" restrictions="0:" /> <ITEM name="weight" value="0" type="double" description="Distances based on relative intensity are weighted by this factor" required="false" advanced="true" restrictions="0:" /> </NODE> </NODE> </NODE> </NODE> <NODE name="6" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="180" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="4" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="20" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" /> <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="edges" description=""> <NODE name="0" description=""> <NODE name="source/target" description=""> <ITEM name="" value="1/3" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="1" description=""> <NODE name="source/target" description=""> <ITEM name="" value="2/3" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="id" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="2" description=""> <NODE name="source/target" description=""> <ITEM name="" value="0/1" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="3" description=""> <NODE name="source/target" description=""> <ITEM name="" value="5/6" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="4" description=""> <NODE name="source/target" description=""> <ITEM name="" value="3/4" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="5" description=""> <NODE name="source/target" description=""> <ITEM name="" value="4/5" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> </NODE> </PARAMETERS>