Mercurial > repos > galaxyp > openms_mapalignmentevaluation

comparison tool.conf @ 0:cf8a65bc9e8a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:40:20 -0500
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-1:000000000000 0:cf8a65bc9e8a
1 <?xml version='1.0' encoding='UTF-8'?>
2 <toolbox>
3 <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction">
4 <tool file="openms/PTModel.xml"/>
5 <tool file="openms/PTPredict.xml"/>
6 <tool file="openms/RTModel.xml"/>
7 <tool file="openms/RTPredict.xml"/>
8 </section>
9 <section id="section-id-DEFAULT" name="DEFAULT">
10 <tool file="openms/OpenSwathFileSplitter.xml"/>
11 <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
12 </section>
13 <section id="section-id-TargetedExperiments" name="Targeted Experiments">
14 <tool file="openms/ConvertTraMLToTSV.xml"/>
15 <tool file="openms/ConvertTSVToTraML.xml"/>
16 <tool file="openms/InclusionExclusionListCreator.xml"/>
17 <tool file="openms/MRMMapper.xml"/>
18 <tool file="openms/OpenSwathAnalyzer.xml"/>
19 <tool file="openms/OpenSwathAssayGenerator.xml"/>
20 <tool file="openms/OpenSwathChromatogramExtractor.xml"/>
21 <tool file="openms/OpenSwathConfidenceScoring.xml"/>
22 <tool file="openms/OpenSwathDecoyGenerator.xml"/>
23 <tool file="openms/OpenSwathDIAPreScoring.xml"/>
24 <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
25 <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
26 <tool file="openms/OpenSwathRTNormalizer.xml"/>
27 <tool file="openms/PrecursorIonSelector.xml"/>
28 </section>
29 <section id="section-id-Utilities" name="Utilities">
30 <tool file="openms/AccurateMassSearch.xml"/>
31 <tool file="openms/CVInspector.xml"/>
32 <tool file="openms/DecoyDatabase.xml"/>
33 <tool file="openms/DeMeanderize.xml"/>
34 <tool file="openms/Digestor.xml"/>
35 <tool file="openms/DigestorMotif.xml"/>
36 <tool file="openms/ERPairFinder.xml"/>
37 <tool file="openms/FFEval.xml"/>
38 <tool file="openms/FuzzyDiff.xml"/>
39 <tool file="openms/IDDecoyProbability.xml"/>
40 <tool file="openms/IDExtractor.xml"/>
41 <tool file="openms/IDMassAccuracy.xml"/>
42 <tool file="openms/IDScoreSwitcher.xml"/>
43 <tool file="openms/IDSplitter.xml"/>
44 <tool file="openms/LabeledEval.xml"/>
45 <tool file="openms/LowMemPeakPickerHiRes.xml"/>
46 <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
47 <tool file="openms/MapAlignmentEvaluation.xml"/>
48 <tool file="openms/MassCalculator.xml"/>
49 <tool file="openms/MetaboliteSpectralMatcher.xml"/>
50 <tool file="openms/MetaProSIP.xml"/>
51 <tool file="openms/MRMPairFinder.xml"/>
52 <tool file="openms/MRMTransitionGroupPicker.xml"/>
53 <tool file="openms/MSSimulator.xml"/>
54 <tool file="openms/MultiplexResolver.xml"/>
55 <tool file="openms/MzMLSplitter.xml"/>
56 <tool file="openms/OpenSwathWorkflow.xml"/>
57 <tool file="openms/QCCalculator.xml"/>
58 <tool file="openms/QCEmbedder.xml"/>
59 <tool file="openms/QCExporter.xml"/>
60 <tool file="openms/QCExtractor.xml"/>
61 <tool file="openms/QCImporter.xml"/>
62 <tool file="openms/QCMerger.xml"/>
63 <tool file="openms/QCShrinker.xml"/>
64 <tool file="openms/RNPxl.xml"/>
65 <tool file="openms/RNPxlXICFilter.xml"/>
66 <tool file="openms/RTEvaluation.xml"/>
67 <tool file="openms/SemanticValidator.xml"/>
68 <tool file="openms/SequenceCoverageCalculator.xml"/>
69 <tool file="openms/SimpleSearchEngine.xml"/>
70 <tool file="openms/SpecLibCreator.xml"/>
71 <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
72 <tool file="openms/TICCalculator.xml"/>
73 <tool file="openms/TopPerc.xml"/>
74 <tool file="openms/TransformationEvaluation.xml"/>
75 <tool file="openms/XMLValidator.xml"/>
76 </section>
77 <section id="section-id-MapAlignment" name="Map Alignment">
78 <tool file="openms/ConsensusMapNormalizer.xml"/>
79 <tool file="openms/FeatureLinkerLabeled.xml"/>
80 <tool file="openms/FeatureLinkerUnlabeled.xml"/>
81 <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
82 <tool file="openms/MapRTTransformer.xml"/>
83 </section>
84 <section id="section-id-IDProcessing" name="ID Processing">
85 <tool file="openms/ConsensusID.xml"/>
86 <tool file="openms/FalseDiscoveryRate.xml"/>
87 <tool file="openms/FidoAdapter.xml"/>
88 <tool file="openms/IDConflictResolver.xml"/>
89 <tool file="openms/IDFileConverter.xml"/>
90 <tool file="openms/IDFilter.xml"/>
91 <tool file="openms/IDMapper.xml"/>
92 <tool file="openms/IDPosteriorErrorProbability.xml"/>
93 <tool file="openms/IDRTCalibration.xml"/>
94 <tool file="openms/LuciphorAdapter.xml"/>
95 <tool file="openms/PeptideIndexer.xml"/>
96 <tool file="openms/PhosphoScoring.xml"/>
97 </section>
98 <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing">
99 <tool file="openms/BaselineFilter.xml"/>
100 <tool file="openms/ExternalCalibration.xml"/>
101 <tool file="openms/HighResPrecursorMassCorrector.xml"/>
102 <tool file="openms/InternalCalibration.xml"/>
103 <tool file="openms/MapNormalizer.xml"/>
104 <tool file="openms/MassTraceExtractor.xml"/>
105 <tool file="openms/NoiseFilterGaussian.xml"/>
106 <tool file="openms/NoiseFilterSGolay.xml"/>
107 <tool file="openms/PeakPickerHiRes.xml"/>
108 <tool file="openms/PeakPickerIterative.xml"/>
109 <tool file="openms/PeakPickerWavelet.xml"/>
110 <tool file="openms/PrecursorMassCorrector.xml"/>
111 <tool file="openms/SpectraMerger.xml"/>
112 <tool file="openms/TOFCalibration.xml"/>
113 </section>
114 <section id="section-id-Identification" name="Identification">
115 <tool file="openms/CompNovoCID.xml"/>
116 <tool file="openms/CompNovo.xml"/>
117 <tool file="openms/InspectAdapter.xml"/>
118 <tool file="openms/MascotAdapter.xml"/>
119 <tool file="openms/MascotAdapterOnline.xml"/>
120 <tool file="openms/MSGFPlusAdapter.xml"/>
121 <tool file="openms/ProteinInference.xml"/>
122 <tool file="openms/SpectraFilterBernNorm.xml"/>
123 <tool file="openms/SpectraFilterMarkerMower.xml"/>
124 <tool file="openms/SpectraFilterNLargest.xml"/>
125 <tool file="openms/SpectraFilterNormalizer.xml"/>
126 <tool file="openms/SpectraFilterParentPeakMower.xml"/>
127 <tool file="openms/SpectraFilterScaler.xml"/>
128 <tool file="openms/SpectraFilterSqrtMower.xml"/>
129 <tool file="openms/SpectraFilterThresholdMower.xml"/>
130 <tool file="openms/SpectraFilterWindowMower.xml"/>
131 <tool file="openms/XTandemAdapter.xml"/>
132 </section>
133 <section id="section-id-FileHandling" name="File Handling">
134 <tool file="openms/DTAExtractor.xml"/>
135 <tool file="openms/FileConverter.xml"/>
136 <tool file="openms/FileFilter.xml"/>
137 <tool file="openms/FileInfo.xml"/>
138 <tool file="openms/FileMerger.xml"/>
139 <tool file="openms/IDMerger.xml"/>
140 <tool file="openms/IDRipper.xml"/>
141 <tool file="openms/MapStatistics.xml"/>
142 <tool file="openms/MzTabExporter.xml"/>
143 <tool file="openms/TextExporter.xml"/>
144 </section>
145 <section id="section-id-Quantitation" name="Quantitation">
146 <tool file="openms/AdditiveSeries.xml"/>
147 <tool file="openms/Decharger.xml"/>
148 <tool file="openms/EICExtractor.xml"/>
149 <tool file="openms/FeatureFinderCentroided.xml"/>
150 <tool file="openms/FeatureFinderIdentification.xml"/>
151 <tool file="openms/FeatureFinderIsotopeWavelet.xml"/>
152 <tool file="openms/FeatureFinderMetabo.xml"/>
153 <tool file="openms/FeatureFinderMRM.xml"/>
154 <tool file="openms/FeatureFinderMultiplex.xml"/>
155 <tool file="openms/FeatureFinderSuperHirn.xml"/>
156 <tool file="openms/IsobaricAnalyzer.xml"/>
157 <tool file="openms/ITRAQAnalyzer.xml"/>
158 <tool file="openms/ProteinQuantifier.xml"/>
159 <tool file="openms/ProteinResolver.xml"/>
160 <tool file="openms/TMTAnalyzer.xml"/>
161 </section>
162 </toolbox>