Mercurial > repos > galaxyp > openms_decoydatabase

comparison tool.conf @ 3:178e00cf12d7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 08:58:49 -0400
parents 53f456ded5a6
children
comparison
equal deleted inserted replaced
2:8ced1ef014ae 3:178e00cf12d7
4 <tool file="openms/PTModel.xml"/> 4 <tool file="openms/PTModel.xml"/>
5 <tool file="openms/PTPredict.xml"/> 5 <tool file="openms/PTPredict.xml"/>
6 <tool file="openms/RTModel.xml"/> 6 <tool file="openms/RTModel.xml"/>
7 <tool file="openms/RTPredict.xml"/> 7 <tool file="openms/RTPredict.xml"/>
8 </section> 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"> 9 <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"/> 10 <tool file="openms/InclusionExclusionListCreator.xml"/>
17 <tool file="openms/MRMMapper.xml"/> 11 <tool file="openms/MRMMapper.xml"/>
18 <tool file="openms/OpenSwathAnalyzer.xml"/> 12 <tool file="openms/OpenSwathAnalyzer.xml"/>
19 <tool file="openms/OpenSwathAssayGenerator.xml"/> 13 <tool file="openms/OpenSwathAssayGenerator.xml"/>
20 <tool file="openms/OpenSwathChromatogramExtractor.xml"/> 14 <tool file="openms/OpenSwathChromatogramExtractor.xml"/>
21 <tool file="openms/OpenSwathConfidenceScoring.xml"/> 15 <tool file="openms/OpenSwathConfidenceScoring.xml"/>
22 <tool file="openms/OpenSwathDecoyGenerator.xml"/> 16 <tool file="openms/OpenSwathDecoyGenerator.xml"/>
23 <tool file="openms/OpenSwathDIAPreScoring.xml"/> 17 <tool file="openms/OpenSwathDIAPreScoring.xml"/>
24 <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> 18 <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
19 <tool file="openms/OpenSwathFileSplitter.xml"/>
20 <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
25 <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> 21 <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
26 <tool file="openms/OpenSwathRTNormalizer.xml"/> 22 <tool file="openms/OpenSwathRTNormalizer.xml"/>
27 <tool file="openms/PrecursorIonSelector.xml"/> 23 <tool file="openms/PrecursorIonSelector.xml"/>
24 <tool file="openms/TargetedFileConverter.xml"/>
28 </section> 25 </section>
29 <section id="section-id-Utilities" name="Utilities"> 26 <section id="section-id-Utilities" name="Utilities">
30 <tool file="openms/AccurateMassSearch.xml"/> 27 <tool file="openms/AccurateMassSearch.xml"/>
31 <tool file="openms/CVInspector.xml"/> 28 <tool file="openms/CVInspector.xml"/>
29 <tool file="openms/DatabaseFilter.xml"/>
32 <tool file="openms/DecoyDatabase.xml"/> 30 <tool file="openms/DecoyDatabase.xml"/>
33 <tool file="openms/DeMeanderize.xml"/> 31 <tool file="openms/DeMeanderize.xml"/>
34 <tool file="openms/Digestor.xml"/> 32 <tool file="openms/Digestor.xml"/>
35 <tool file="openms/DigestorMotif.xml"/> 33 <tool file="openms/DigestorMotif.xml"/>
36 <tool file="openms/ERPairFinder.xml"/> 34 <tool file="openms/ERPairFinder.xml"/>
42 <tool file="openms/IDScoreSwitcher.xml"/> 40 <tool file="openms/IDScoreSwitcher.xml"/>
43 <tool file="openms/IDSplitter.xml"/> 41 <tool file="openms/IDSplitter.xml"/>
44 <tool file="openms/LabeledEval.xml"/> 42 <tool file="openms/LabeledEval.xml"/>
45 <tool file="openms/LowMemPeakPickerHiRes.xml"/> 43 <tool file="openms/LowMemPeakPickerHiRes.xml"/>
46 <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> 44 <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
47 <tool file="openms/MapAlignmentEvaluation.xml"/>
48 <tool file="openms/MassCalculator.xml"/> 45 <tool file="openms/MassCalculator.xml"/>
49 <tool file="openms/MetaboliteSpectralMatcher.xml"/> 46 <tool file="openms/MetaboliteSpectralMatcher.xml"/>
50 <tool file="openms/MetaProSIP.xml"/> 47 <tool file="openms/MetaProSIP.xml"/>
51 <tool file="openms/MRMPairFinder.xml"/> 48 <tool file="openms/MRMPairFinder.xml"/>
52 <tool file="openms/MRMTransitionGroupPicker.xml"/> 49 <tool file="openms/MRMTransitionGroupPicker.xml"/>
60 <tool file="openms/QCExtractor.xml"/> 57 <tool file="openms/QCExtractor.xml"/>
61 <tool file="openms/QCImporter.xml"/> 58 <tool file="openms/QCImporter.xml"/>
62 <tool file="openms/QCMerger.xml"/> 59 <tool file="openms/QCMerger.xml"/>
63 <tool file="openms/QCShrinker.xml"/> 60 <tool file="openms/QCShrinker.xml"/>
64 <tool file="openms/RNPxl.xml"/> 61 <tool file="openms/RNPxl.xml"/>
62 <tool file="openms/RNPxlSearch.xml"/>
65 <tool file="openms/RNPxlXICFilter.xml"/> 63 <tool file="openms/RNPxlXICFilter.xml"/>
66 <tool file="openms/RTEvaluation.xml"/> 64 <tool file="openms/RTEvaluation.xml"/>
67 <tool file="openms/SemanticValidator.xml"/> 65 <tool file="openms/SemanticValidator.xml"/>
68 <tool file="openms/SequenceCoverageCalculator.xml"/> 66 <tool file="openms/SequenceCoverageCalculator.xml"/>
69 <tool file="openms/SimpleSearchEngine.xml"/> 67 <tool file="openms/SimpleSearchEngine.xml"/>
70 <tool file="openms/SpecLibCreator.xml"/> 68 <tool file="openms/SpecLibCreator.xml"/>
69 <tool file="openms/SpectraSTSearchAdapter.xml"/>
71 <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> 70 <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
72 <tool file="openms/TICCalculator.xml"/> 71 <tool file="openms/TICCalculator.xml"/>
73 <tool file="openms/TopPerc.xml"/> 72 <tool file="openms/TopPerc.xml"/>
74 <tool file="openms/TransformationEvaluation.xml"/> 73 <tool file="openms/TransformationEvaluation.xml"/>
75 <tool file="openms/XMLValidator.xml"/> 74 <tool file="openms/XMLValidator.xml"/>
76 </section> 75 </section>
77 <section id="section-id-MapAlignment" name="Map Alignment"> 76 <section id="section-id-MapAlignment" name="Map Alignment">
78 <tool file="openms/ConsensusMapNormalizer.xml"/> 77 <tool file="openms/ConsensusMapNormalizer.xml"/>
79 <tool file="openms/FeatureLinkerLabeled.xml"/> 78 <tool file="openms/FeatureLinkerLabeled.xml"/>
80 <tool file="openms/FeatureLinkerUnlabeled.xml"/> 79 <tool file="openms/FeatureLinkerUnlabeled.xml"/>
80 <tool file="openms/FeatureLinkerUnlabeledKD.xml"/>
81 <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> 81 <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
82 <tool file="openms/MapRTTransformer.xml"/> 82 <tool file="openms/MapRTTransformer.xml"/>
83 </section> 83 </section>
84 <section id="section-id-IDProcessing" name="ID Processing"> 84 <section id="section-id-IDProcessing" name="ID Processing">
85 <tool file="openms/ConsensusID.xml"/> 85 <tool file="openms/ConsensusID.xml"/>
152 <tool file="openms/FeatureFinderMetabo.xml"/> 152 <tool file="openms/FeatureFinderMetabo.xml"/>
153 <tool file="openms/FeatureFinderMRM.xml"/> 153 <tool file="openms/FeatureFinderMRM.xml"/>
154 <tool file="openms/FeatureFinderMultiplex.xml"/> 154 <tool file="openms/FeatureFinderMultiplex.xml"/>
155 <tool file="openms/FeatureFinderSuperHirn.xml"/> 155 <tool file="openms/FeatureFinderSuperHirn.xml"/>
156 <tool file="openms/IsobaricAnalyzer.xml"/> 156 <tool file="openms/IsobaricAnalyzer.xml"/>
157 <tool file="openms/ITRAQAnalyzer.xml"/>
158 <tool file="openms/ProteinQuantifier.xml"/> 157 <tool file="openms/ProteinQuantifier.xml"/>
159 <tool file="openms/ProteinResolver.xml"/> 158 <tool file="openms/ProteinResolver.xml"/>
160 <tool file="openms/TMTAnalyzer.xml"/>
161 </section> 159 </section>
162 </toolbox> 160 </toolbox>