Mercurial > repos > galaxyp > openms_converttramltotsv

annotate tool.conf @ 2:e66eba918cf0 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
author galaxyp
date Thu, 27 Apr 2017 13:17:13 -0400
parents 5d0e9de15ab1
children
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5d0e9de15ab1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <toolbox>
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3 <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction">
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4 <tool file="openms/PTModel.xml"/>
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5 <tool file="openms/PTPredict.xml"/>
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6 <tool file="openms/RTModel.xml"/>
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7 <tool file="openms/RTPredict.xml"/>
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8 </section>
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9 <section id="section-id-DEFAULT" name="DEFAULT">
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10 <tool file="openms/OpenSwathFileSplitter.xml"/>
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11 <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
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12 </section>
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13 <section id="section-id-TargetedExperiments" name="Targeted Experiments">
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14 <tool file="openms/ConvertTraMLToTSV.xml"/>
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15 <tool file="openms/ConvertTSVToTraML.xml"/>
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16 <tool file="openms/InclusionExclusionListCreator.xml"/>
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17 <tool file="openms/MRMMapper.xml"/>
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18 <tool file="openms/OpenSwathAnalyzer.xml"/>
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19 <tool file="openms/OpenSwathAssayGenerator.xml"/>
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20 <tool file="openms/OpenSwathChromatogramExtractor.xml"/>
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21 <tool file="openms/OpenSwathConfidenceScoring.xml"/>
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22 <tool file="openms/OpenSwathDecoyGenerator.xml"/>
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23 <tool file="openms/OpenSwathDIAPreScoring.xml"/>
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24 <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
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25 <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
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26 <tool file="openms/OpenSwathRTNormalizer.xml"/>
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27 <tool file="openms/PrecursorIonSelector.xml"/>
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28 </section>
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29 <section id="section-id-Utilities" name="Utilities">
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30 <tool file="openms/AccurateMassSearch.xml"/>
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31 <tool file="openms/CVInspector.xml"/>
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32 <tool file="openms/DecoyDatabase.xml"/>
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33 <tool file="openms/DeMeanderize.xml"/>
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34 <tool file="openms/Digestor.xml"/>
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35 <tool file="openms/DigestorMotif.xml"/>
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36 <tool file="openms/ERPairFinder.xml"/>
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37 <tool file="openms/FFEval.xml"/>
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38 <tool file="openms/FuzzyDiff.xml"/>
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39 <tool file="openms/IDDecoyProbability.xml"/>
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40 <tool file="openms/IDExtractor.xml"/>
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41 <tool file="openms/IDMassAccuracy.xml"/>
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42 <tool file="openms/IDScoreSwitcher.xml"/>
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43 <tool file="openms/IDSplitter.xml"/>
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44 <tool file="openms/LabeledEval.xml"/>
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45 <tool file="openms/LowMemPeakPickerHiRes.xml"/>
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46 <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
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47 <tool file="openms/MapAlignmentEvaluation.xml"/>
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48 <tool file="openms/MassCalculator.xml"/>
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49 <tool file="openms/MetaboliteSpectralMatcher.xml"/>
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50 <tool file="openms/MetaProSIP.xml"/>
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51 <tool file="openms/MRMPairFinder.xml"/>
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52 <tool file="openms/MRMTransitionGroupPicker.xml"/>
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53 <tool file="openms/MSSimulator.xml"/>
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54 <tool file="openms/MultiplexResolver.xml"/>
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55 <tool file="openms/MzMLSplitter.xml"/>
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56 <tool file="openms/OpenSwathWorkflow.xml"/>
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57 <tool file="openms/QCCalculator.xml"/>
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58 <tool file="openms/QCEmbedder.xml"/>
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59 <tool file="openms/QCExporter.xml"/>
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60 <tool file="openms/QCExtractor.xml"/>
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61 <tool file="openms/QCImporter.xml"/>
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62 <tool file="openms/QCMerger.xml"/>
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63 <tool file="openms/QCShrinker.xml"/>
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64 <tool file="openms/RNPxl.xml"/>
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65 <tool file="openms/RNPxlXICFilter.xml"/>
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66 <tool file="openms/RTEvaluation.xml"/>
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67 <tool file="openms/SemanticValidator.xml"/>
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68 <tool file="openms/SequenceCoverageCalculator.xml"/>
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69 <tool file="openms/SimpleSearchEngine.xml"/>
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70 <tool file="openms/SpecLibCreator.xml"/>
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71 <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
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72 <tool file="openms/TICCalculator.xml"/>
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73 <tool file="openms/TopPerc.xml"/>
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74 <tool file="openms/TransformationEvaluation.xml"/>
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75 <tool file="openms/XMLValidator.xml"/>
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76 </section>
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77 <section id="section-id-MapAlignment" name="Map Alignment">
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78 <tool file="openms/ConsensusMapNormalizer.xml"/>
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79 <tool file="openms/FeatureLinkerLabeled.xml"/>
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80 <tool file="openms/FeatureLinkerUnlabeled.xml"/>
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81 <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
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82 <tool file="openms/MapRTTransformer.xml"/>
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83 </section>
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84 <section id="section-id-IDProcessing" name="ID Processing">
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85 <tool file="openms/ConsensusID.xml"/>
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86 <tool file="openms/FalseDiscoveryRate.xml"/>
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87 <tool file="openms/FidoAdapter.xml"/>
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88 <tool file="openms/IDConflictResolver.xml"/>
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89 <tool file="openms/IDFileConverter.xml"/>
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90 <tool file="openms/IDFilter.xml"/>
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91 <tool file="openms/IDMapper.xml"/>
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92 <tool file="openms/IDPosteriorErrorProbability.xml"/>
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93 <tool file="openms/IDRTCalibration.xml"/>
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94 <tool file="openms/LuciphorAdapter.xml"/>
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95 <tool file="openms/PeptideIndexer.xml"/>
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96 <tool file="openms/PhosphoScoring.xml"/>
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97 </section>
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98 <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing">
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99 <tool file="openms/BaselineFilter.xml"/>
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100 <tool file="openms/ExternalCalibration.xml"/>
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101 <tool file="openms/HighResPrecursorMassCorrector.xml"/>
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102 <tool file="openms/InternalCalibration.xml"/>
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103 <tool file="openms/MapNormalizer.xml"/>
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104 <tool file="openms/MassTraceExtractor.xml"/>
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105 <tool file="openms/NoiseFilterGaussian.xml"/>
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106 <tool file="openms/NoiseFilterSGolay.xml"/>
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107 <tool file="openms/PeakPickerHiRes.xml"/>
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108 <tool file="openms/PeakPickerIterative.xml"/>
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109 <tool file="openms/PeakPickerWavelet.xml"/>
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110 <tool file="openms/PrecursorMassCorrector.xml"/>
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111 <tool file="openms/SpectraMerger.xml"/>
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112 <tool file="openms/TOFCalibration.xml"/>
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113 </section>
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114 <section id="section-id-Identification" name="Identification">
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115 <tool file="openms/CompNovoCID.xml"/>
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116 <tool file="openms/CompNovo.xml"/>
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117 <tool file="openms/InspectAdapter.xml"/>
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118 <tool file="openms/MascotAdapter.xml"/>
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119 <tool file="openms/MascotAdapterOnline.xml"/>
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120 <tool file="openms/MSGFPlusAdapter.xml"/>
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121 <tool file="openms/ProteinInference.xml"/>
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122 <tool file="openms/SpectraFilterBernNorm.xml"/>
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123 <tool file="openms/SpectraFilterMarkerMower.xml"/>
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124 <tool file="openms/SpectraFilterNLargest.xml"/>
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125 <tool file="openms/SpectraFilterNormalizer.xml"/>
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126 <tool file="openms/SpectraFilterParentPeakMower.xml"/>
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127 <tool file="openms/SpectraFilterScaler.xml"/>
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128 <tool file="openms/SpectraFilterSqrtMower.xml"/>
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129 <tool file="openms/SpectraFilterThresholdMower.xml"/>
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130 <tool file="openms/SpectraFilterWindowMower.xml"/>
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131 <tool file="openms/XTandemAdapter.xml"/>
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132 </section>
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133 <section id="section-id-FileHandling" name="File Handling">
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134 <tool file="openms/DTAExtractor.xml"/>
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135 <tool file="openms/FileConverter.xml"/>
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136 <tool file="openms/FileFilter.xml"/>
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137 <tool file="openms/FileInfo.xml"/>
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138 <tool file="openms/FileMerger.xml"/>
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139 <tool file="openms/IDMerger.xml"/>
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140 <tool file="openms/IDRipper.xml"/>
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141 <tool file="openms/MapStatistics.xml"/>
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142 <tool file="openms/MzTabExporter.xml"/>
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143 <tool file="openms/TextExporter.xml"/>
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144 </section>
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145 <section id="section-id-Quantitation" name="Quantitation">
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146 <tool file="openms/AdditiveSeries.xml"/>
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147 <tool file="openms/Decharger.xml"/>
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148 <tool file="openms/EICExtractor.xml"/>
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149 <tool file="openms/FeatureFinderCentroided.xml"/>
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150 <tool file="openms/FeatureFinderIdentification.xml"/>
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151 <tool file="openms/FeatureFinderIsotopeWavelet.xml"/>
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152 <tool file="openms/FeatureFinderMetabo.xml"/>
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153 <tool file="openms/FeatureFinderMRM.xml"/>
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154 <tool file="openms/FeatureFinderMultiplex.xml"/>
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155 <tool file="openms/FeatureFinderSuperHirn.xml"/>
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156 <tool file="openms/IsobaricAnalyzer.xml"/>
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157 <tool file="openms/ITRAQAnalyzer.xml"/>
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158 <tool file="openms/ProteinQuantifier.xml"/>
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159 <tool file="openms/ProteinResolver.xml"/>
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160 <tool file="openms/TMTAnalyzer.xml"/>
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161 </section>
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162 </toolbox>