Mercurial > repos > jjohnson > peptideshaker

annotate test-data/Identification_Parameters_default.par @ 0:8b99cb00e1c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
author jjohnson
date Tue, 15 May 2018 14:50:35 -0400
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8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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1 {
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2 "marshallableParameterType": "identification_parameters",
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3 "name": "SEARCHGUI_IdentificationParameters",
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4 "description": "DB: dataset_118.dat.\n",
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5 "defaultDescription": true,
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6 "searchParameters": {
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7 "precursorAccuracyType": "PPM",
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8 "fragmentAccuracyType": "DA",
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9 "precursorTolerance": 10.0,
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10 "precursorToleranceDalton": 0.5,
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11 "fragmentIonMZTolerance": 0.5,
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12 "ptmSettings": {
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13 "fixedModifications": [],
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14 "variableModifications": [],
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15 "refinementVariableModifications": [],
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16 "refinementFixedModifications": [],
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17 "colors": {},
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18 "backUp": {}
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19 },
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20 "nMissedCleavages": 2,
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21 "digestionPreferences": {
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22 "cleavagePreference": "enzyme",
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23 "enzymes": [
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24 {
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25 "id": 0,
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26 "name": "Trypsin",
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27 "aminoAcidBefore": [],
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28 "aminoAcidAfter": [],
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29 "restrictionBefore": [],
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30 "restrictionAfter": [],
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31 "aminoAcidBeforeSet": [
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32 "R",
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33 "K"
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34 ],
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35 "aminoAcidAfterSet": [],
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36 "restrictionBeforeSet": [],
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37 "restrictionAfterSet": [
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38 "P"
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39 ],
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40 "isSemiSpecific": false,
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41 "isWholeProtein": false,
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42 "cvTerm": {
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43 "ontology": "PSI-MS",
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44 "accession": "MS:1001251",
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45 "name": "Trypsin"
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46 }
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47 }
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48 ],
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49 "nMissedCleavages": {
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50 "Trypsin": 2
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51 },
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52 "specificity": {
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53 "Trypsin": "specific"
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54 }
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55 },
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56 "fastaFile": {
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57 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
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58 },
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59 "parametersFile": {},
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60 "forwardIons": [
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61 1
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62 ],
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63 "rewindIons": [
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64 4
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65 ],
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66 "minChargeSearched": {
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67 "sign": 1,
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68 "value": 2
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69 },
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70 "maxChargeSearched": {
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71 "sign": 1,
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72 "value": 4
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73 },
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74 "minIsotopicCorrection": 0,
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75 "maxIsotopicCorrection": 1,
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76 "refMass": 2000.0,
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77 "algorithmParameters": {
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78 "1": {
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79 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters",
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80 "data": {
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81 "maxEValue": 100.0,
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82 "hitListLength": 10,
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83 "minimalChargeForMultipleChargedFragments": {
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diff changeset
84 "sign": 1,
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jjohnson
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diff changeset
85 "value": 3
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jjohnson
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diff changeset
86 },
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jjohnson
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diff changeset
87 "minPeptideLength": 8,
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jjohnson
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88 "maxPeptideLength": 30,
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jjohnson
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diff changeset
89 "removePrecursor": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
90 "scalePrecursor": true,
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91 "estimateCharge": true,
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92 "selectedOutput": "OMX",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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93 "memoryMappedSequenceLibraries": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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94 "numberOfItotopicPeaks": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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95 "neutronThreshold": 1446.94,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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96 "lowIntensityCutOff": 0.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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97 "highIntensityCutOff": 0.2,
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jjohnson
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98 "intensityCutOffIncrement": 5.0E-4,
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jjohnson
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99 "singleChargeWindow": 27,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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100 "doubleChargeWindow": 14,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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101 "nPeaksInSingleChargeWindow": 2,
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jjohnson
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102 "nPeaksInDoubleChargeWindow": 2,
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103 "maxHitsPerSpectrumPerCharge": 30,
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jjohnson
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104 "nAnnotatedMostIntensePeaks": 6,
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jjohnson
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105 "minAnnotatedPeaks": 2,
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106 "minPeaks": 4,
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jjohnson
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107 "cleaveNtermMethionine": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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108 "maxMzLadders": 128,
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109 "maxFragmentCharge": 2,
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jjohnson
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110 "fractionOfPeaksForChargeEstimation": 0.95,
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111 "determineChargePlusOneAlgorithmically": true,
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112 "searchPositiveIons": true,
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jjohnson
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113 "minPrecPerSpectrum": 1,
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jjohnson
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114 "searchForwardFragmentFirst": false,
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jjohnson
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115 "searchRewindFragments": true,
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116 "maxFragmentPerSeries": 100,
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117 "useCorrelationCorrectionScore": true,
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jjohnson
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118 "consecutiveIonProbability": 0.5,
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jjohnson
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119 "iterativeSequenceEvalue": 0.0,
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120 "iterativeReplaceEvalue": 0.0,
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jjohnson
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121 "iterativeSpectrumEvalue": 0.01,
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jjohnson
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122 "noProlineRuleSeries": [],
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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123 "ptmIndexes": {}
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124 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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125 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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126 "2": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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127 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters",
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128 "data": {
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129 "maxEValue": 0.01,
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130 "outputResults": "all",
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131 "dynamicRange": 100.0,
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132 "nPeaks": 50,
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133 "minPrecursorMass": 500.0,
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134 "minFragmentMz": 200.0,
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135 "minPeaksPerSpectrum": 5,
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136 "proteinQuickAcetyl": true,
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137 "quickPyrolidone": true,
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138 "refine": true,
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139 "refineSemi": false,
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140 "refinePointMutations": false,
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141 "refineSpectrumSynthesis": true,
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142 "refineUnanticipatedCleavages": true,
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143 "refineSnaps": true,
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144 "maximumExpectationValueRefinement": 0.01,
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145 "potentialModificationsForFullRefinment": false,
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146 "skylinePath": "",
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147 "outputProteins": true,
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148 "outputSequences": false,
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149 "outputSpectra": true,
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150 "outputHistograms": false,
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151 "stpBias": false,
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152 "useNoiseSuppression": false,
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153 "proteinPtmComplexity": 6.0
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154 }
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155 },
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156 "3": {
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157 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters",
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158 "data": {
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159 "hitListLength": 10,
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160 "estimateCharge": true,
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161 "correctPrecursorMass": false,
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162 "discardLowQualitySpectra": true,
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163 "fragmentationModel": "CID_IT_TRYP",
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164 "generateQuery": false
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165 }
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166 },
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167 "4": {
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168 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters",
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169 "data": {
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170 "maxPeptideMass": 4600.0,
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171 "maxCombinations": 250,
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172 "topPeaks": 8,
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173 "topPeaksWindow": 100,
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174 "includeWater": true,
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175 "includeAmmonia": true,
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176 "dependentLosses": true,
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177 "fragmentAll": false,
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178 "empiricalCorrection": true,
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179 "higherCharge": true,
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180 "fragmentationMethod": "CID",
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181 "maxNumberOfModifications": 5,
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182 "minPeptideLengthNoEnzyme": 8,
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183 "maxPeptideLengthNoEnzyme": 25,
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184 "equalIL": false,
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185 "numberOfCandidates": 10,
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186 "ptmIndexes": {},
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187 "decoyMode": "none"
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188 }
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189 },
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190 "5": {
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191 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters",
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192 "data": {
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193 "generateDecoy": false,
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194 "instrumentID": "b, y",
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195 "maxRank": 10,
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196 "monoisotopic": true,
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197 "lowMemoryMode": true
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198 }
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199 },
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200 "7": {
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201 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters",
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202 "data": {
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203 "searchDecoyDatabase": false,
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204 "instrumentID": 3,
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205 "fragmentationType": 3,
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206 "protocol": 0,
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207 "minPeptideLength": 8,
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208 "maxPeptideLength": 30,
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209 "numberOfSpectrumMarches": 10,
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210 "additionalOutput": false,
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211 "lowerIsotopeErrorRange": -1,
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212 "upperIsotopeErrorRange": 2,
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213 "numberTolerableTermini": 2,
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214 "numberOfPtmsPerPeptide": 2
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215 }
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216 },
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217 "8": {
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218 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters",
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219 "data": {
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220 "ticCutoffPercentage": 100.0,
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221 "maxPeakCount": 100,
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222 "numIntensityClasses": 3,
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223 "adjustPrecursorMass": false,
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224 "minPrecursorAdjustment": -0.5,
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225 "maxPrecursorAdjustment": 1.5,
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226 "precursorAdjustmentStep": 0.1,
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227 "numChargeStates": 3,
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228 "outputSuffix": "",
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229 "useChargeStateFromMS": true,
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230 "duplicateSpectra": true,
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231 "deisotopingMode": 0,
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232 "isotopeMzTolerance": 0.25,
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233 "complementMzTolerance": 0.1,
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234 "tagLength": 4,
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235 "maxDynamicMods": 2,
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236 "maxTagCount": 10,
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237 "intensityScoreWeight": 1.0,
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238 "mzFidelityScoreWeight": 1.0,
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239 "complementScoreWeight": 1.0,
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240 "variablePtms": []
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241 }
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242 },
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243 "10": {
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244 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters",
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245 "data": {
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246 "numberOfSpectrumMatches": 10,
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247 "maxVariableMods": 10,
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248 "requireVariableMods": false,
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249 "minPeaks": 10,
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250 "minPeakIntensity": 0.0,
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251 "removePrecursor": 0,
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252 "removePrecursorTolerance": 1.5,
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253 "lowerClearMzRange": 0.0,
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254 "upperClearMzRange": 0.0,
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255 "enzymeType": 2,
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256 "isotopeCorrection": 1,
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257 "minPrecursorMass": 600.0,
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258 "maxPrecursorMass": 5000.0,
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259 "maxFragmentCharge": 3,
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260 "removeMethionine": false,
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261 "batchSize": 0,
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262 "theoreticalFragmentIonsSumOnly": false,
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263 "fragmentBinOffset": 0.0,
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264 "useSparseMatrix": true,
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265 "selectedOutputFormat": "PepXML",
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266 "printExpectScore": true
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267 }
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268 },
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269 "27": {
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270 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters",
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271 "data": {
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272 "numberOfPeptides": 10,
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273 "lowerPrecursorMass": 300,
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274 "upperPrecursorMass": 5000,
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275 "acticationType": "HCD"
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276 }
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277 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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278 "28": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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279 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters",
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280 "data": {
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281 "fastIndexFolderName": "fasta-index",
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282 "maxVariablePtmsPerTypePerPeptide": 2,
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283 "minPeptideLength": 6,
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284 "maxPeptideLength": 30,
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285 "minPrecursorMass": 200.0,
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286 "maxPrecursorMass": 7200.0,
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287 "decoyFormat": "none",
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288 "keepTerminalAminoAcids": "NC",
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jjohnson
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289 "decoySeed": 1,
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290 "outputFolderName": "crux-output",
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291 "printPeptides": false,
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292 "verbosity": 30,
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293 "monoisotopicPrecursor": true,
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294 "clipNtermMethionine": false,
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295 "digestionType": "full-digest",
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296 "computeSpScore": false,
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297 "numberOfSpectrumMatches": 10,
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298 "computeExactPValues": false,
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299 "minSpectrumMz": 0.0,
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300 "minSpectrumPeaks": 20,
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301 "spectrumCharges": "all",
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302 "removePrecursor": false,
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303 "removePrecursorTolerance": 1.5,
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304 "printProgressIndicatorSize": 1000,
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305 "useFlankingPeaks": false,
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306 "useNeutralLossPeaks": false,
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307 "mzBinWidth": 0.02,
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308 "mzBinOffset": 0.0,
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309 "concatenateTargetDecoy": false,
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310 "textOutput": true,
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311 "sqtOutput": false,
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312 "pepXmlOutput": false,
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313 "mzidOutput": false,
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314 "pinOutput": false,
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315 "removeTempFolders": true
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316 }
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317 },
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318 "13": {
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319 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters",
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320 "data": {
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321 "minPeptideLength": 8,
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322 "maxPeptideLength": 30,
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323 "numberOfSpectrumMatches": 10,
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324 "ticCutoffPercentage": 0.98,
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325 "maxDynamicMods": 2,
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326 "minTerminiCleavages": 2,
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327 "minPrecursorMass": 600.0,
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328 "maxPrecursorMass": 5000.0,
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329 "useSmartPlusThreeModel": true,
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330 "computeXCorr": false,
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331 "numIntensityClasses": 3,
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332 "classSizeMultiplier": 2,
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diff changeset
333 "numberOfBatches": 50,
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334 "lowerIsotopeCorrection": -1,
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335 "upperIsotopeCorrection": 2,
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336 "fragmentationRule": "CID",
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337 "maxPeakCount": 300,
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338 "outputFormat": "mzIdentML"
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339 }
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340 },
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341 "29": {
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342 "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters",
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343 "data": {
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344 "fragmentationMethod": "HCD",
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345 "massAnalyzer": "FT"
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346 }
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347 }
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348 }
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349 },
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350 "annotationSettings": {
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351 "yAxisZoomExcludesBackgroundPeaks": true,
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352 "showAllPeaks": false,
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353 "intensityThresholdType": "percentile",
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354 "intensityLimit": 0.75,
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355 "automaticAnnotation": true,
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356 "selectedIonsMap": {
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357 "TAG_FRAGMENT_ION": [
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360 ],
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361 "REPORTER_ION": [],
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362 "RELATED_ION": [
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383 "PEPTIDE_FRAGMENT_ION": [
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387 "PRECURSOR_ION": [
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390 "IMMONIUM_ION": [
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412 ]
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413 },
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416 "composition": {
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417 "atomChain": [
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418 {
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419 "atomSymbol": "H",
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420 "isotope": 0
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421 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
422 {
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423 "atomSymbol": "H",
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424 "isotope": 0
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jjohnson
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425 },
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426 {
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427 "atomSymbol": "O",
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428 "isotope": 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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429 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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430 ],
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jjohnson
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431 "mass1": -1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
432 "stringValue1": "H(2)O"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
433 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
434 "name": "H2O",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
435 "fixed": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
436 "aminoAcids": [
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
437 "D",
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jjohnson
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438 "E",
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jjohnson
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439 "S",
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jjohnson
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440 "T"
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jjohnson
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diff changeset
441 ]
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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442 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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443 {
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jjohnson
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diff changeset
444 "composition": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
445 "atomChain": [
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
446 {
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jjohnson
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447 "atomSymbol": "N",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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448 "isotope": 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
449 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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450 {
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jjohnson
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451 "atomSymbol": "H",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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452 "isotope": 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
453 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
454 {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
455 "atomSymbol": "H",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
456 "isotope": 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
457 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
458 {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
459 "atomSymbol": "H",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
460 "isotope": 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
461 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
462 ],
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
463 "mass1": -1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
464 "stringValue1": "H(3)N"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
465 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
466 "name": "NH3",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
467 "fixed": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
468 "aminoAcids": [
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
469 "K",
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jjohnson
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diff changeset
470 "N",
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jjohnson
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diff changeset
471 "Q",
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jjohnson
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diff changeset
472 "R"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
473 ]
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
474 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
475 ],
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
476 "neutralLossesAuto": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
477 "reporterIons": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
478 "relatedIons": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
479 "fragmentIonAccuracy": 0.5,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
480 "fragmentIonPpm": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
481 "showForwardIonDeNovoTags": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
482 "showRewindIonDeNovoTags": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
483 "deNovoCharge": 1,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
484 "highResolutionAnnotation": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
485 "tiesResolution": "mostAccurateMz"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
486 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
487 "sequenceMatchingPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
488 "sequenceMatchingType": "indistiguishableAminoAcids",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
489 "limitX": 0.25,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
490 "peptideMapperType": "fm_index"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
491 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
492 "peptideVariantsPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
493 "useSpecificCount": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
494 "nVariants": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
495 "nAaDeletions": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
496 "nAaInsertions": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
497 "nAaSubstitutions": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
498 "nAaSwap": 0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
499 "aaSubstitutionMatrix": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
500 "name": "No Substitution",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
501 "description": "No substitution",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
502 "substitutions": {},
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
503 "reverseMap": {}
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
504 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
505 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
506 "genePreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
507 "autoUpdate": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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508 "useGeneMapping": false
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509 },
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510 "psmScoringPreferences": {
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511 "spectrumMatchingScores": {
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512 "8": [
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jjohnson
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513 1
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514 ],
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515 "3": [
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516 1
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517 ],
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jjohnson
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518 "27": [
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jjohnson
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519 1
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520 ]
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521 },
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522 "defaultScores": [
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523 -1
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524 ],
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525 "minDecoysInBin": 10
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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526 },
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jjohnson
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527 "peptideAssumptionFilter": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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528 "minPepLength": 8,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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529 "maxPepLength": 30,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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530 "maxMassDeviation": 10.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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531 "isPpm": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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532 "unknownPtm": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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533 "minIsotopes": 0,
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534 "maxIsotopes": 1
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jjohnson
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diff changeset
535 },
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jjohnson
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536 "ptmScoringPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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537 "flr": 1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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538 "probabilitsticScoreCalculation": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
539 "selectedProbabilisticScore": "PhosphoRS",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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540 "estimateFlr": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
541 "probabilisticScoreThreshold": 95.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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542 "probabilisticScoreNeutralLosses": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
543 "sequenceMatchingPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
544 "sequenceMatchingType": "aminoAcid",
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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545 "limitX": 0.25,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
546 "peptideMapperType": "fm_index"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
547 },
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jjohnson
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diff changeset
548 "alignNonConfidentPTMs": true
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
549 },
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jjohnson
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diff changeset
550 "proteinInferencePreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
551 "proteinSequenceDatabase": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
552 "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
553 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
554 "simplifyProteinGroups": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
555 "simplifyGroupsScore": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
556 "simplifyGroupsEvidence": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
557 "simplifyGroupsEnzymaticity": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
558 "simplifyGroupsUncharacterized": true
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
559 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
560 "idValidationPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
561 "defaultProteinFDR": 1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
562 "defaultPeptideFDR": 1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
563 "defaultPsmFDR": 1.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
564 "separatePeptides": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
565 "separatePsms": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
566 "mergeSmallSubgroups": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
567 "validationQCPreferences": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
568 "dbSize": false,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
569 "firstDecoy": true,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
570 "confidenceMargin": 1.0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
571 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
572 },
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
573 "fractionSettings": {
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
574 "proteinConfidenceMwPlots": 95.0,
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
575 "fractionMolecularWeightRanges": {}
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
576 }
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
577 }