Mercurial > repos > jjohnson > spectrast

annotate spectrast_params.py @ 4:c9bfe6adb7cd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
author jjohnson
date Wed, 25 Jul 2018 14:41:20 -0400
parents 7f02fc51bddf
children 274fdc50169b
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e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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1 #!/usr/bin/env python
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
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2
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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3 from __future__ import print_function
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
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4
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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5 import argparse
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
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6 import re
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
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7 import sys
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
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8
3
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9 create_opts = [
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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10 'outputFileName',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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11 'useProbTable',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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12 'useProteinList',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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13 'printMRMTable',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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14 'remark',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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15 'binaryFormat',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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16 'writeDtaFiles',
4
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
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17 'writeMgfFile',
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
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18 'writePAIdent',
3
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19 'removeDecoyProteins',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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20 'plotSpectra',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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21 'minimumProbabilityToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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22 'maximumFDRToInclude',
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23 'datasetName',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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24 'setFragmentation',
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25 'setDeamidatedNXST',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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26 'addMzXMLFileToDatasetName',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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27 'centroidPeaks',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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28 'rawSpectraNoiseThreshold',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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29 'rawSpectraMaxDynamicRange',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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30 'minimumNumAAToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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31 'minimumNumPeaksToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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32 'skipRawAnnotation',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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33 'minimumDeltaCnToInclude',
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34 'maximumMassDiffToInclude',
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35 'bracketSpectra',
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36 'mergeBracket',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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37 'filterCriteria',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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38 'combineAction',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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39 'buildAction',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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40 'refreshDatabase',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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41 'reduceSpectra',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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42 'refreshDeleteUnmapped',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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43 'refreshDeleteMultimapped',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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44 'reannotatePeaks',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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45 'minimumMRMQ3MZ',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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46 'maximumMRMQ3MZ',
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47 'refreshTrypticOnly',
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48 'minimumNumReplicates',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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49 'removeDissimilarReplicates',
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50 'peakQuorum',
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51 'maximumNumPeaksUsed',
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52 'maximumNumReplicates',
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53 'maximumNumPeaksKept',
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54 'replicateWeight',
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55 'recordRawSpectra',
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56 'minimumNumReplicates',
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57 'qualityLevelRemove,',
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58 'qualityPenalizeSingletons',
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59 'qualityImmuneProbThreshold',
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60 'qualityImmuneMultipleEngines',
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61 'useBayesianDenoiser',
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62 'trainBayesianDenoiser',
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63 'denoiserMinimumSignalProb',
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64 'denoiserParamFile',
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65 'decoyConcatenate',
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66 'decoySizeRatio',
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67 'decoyPrecursorSwap',
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68 'normalizeRTWithLandmarks',
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69 'normalizeRTLinearRegression',
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70 'unidentifiedClusterIndividualRun',
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71 'unidentifiedClusterMinimumDot',
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72 'unidentifiedRemoveSinglyCharged',
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73 'unidentifiedMinimumNumPeaksToInclude',
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74 'unidentifiedSingletonXreaThreshold',
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75 'allowableModTokens'
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76 ]
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77
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78 filter_opts = [
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79 'outputFileName',
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80 'useProbTable',
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81 'useProteinList',
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82 'printMRMTable',
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83 'remark',
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84 'binaryFormat',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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85 'writeDtaFiles',
4
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
jjohnson
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diff changeset
86 'writeMgfFile',
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty
jjohnson
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diff changeset
87 'writePAIdent',
3
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
88 'removeDecoyProteins',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
89 'plotSpectra',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
90 'minimumProbabilityToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
91 'maximumFDRToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
92 'datasetName',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
93 'setFragmentation',
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jjohnson
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diff changeset
94 'setDeamidatedNXST',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
95 'addMzXMLFileToDatasetName',
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jjohnson
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diff changeset
96 'centroidPeaks',
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jjohnson
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diff changeset
97 'rawSpectraNoiseThreshold',
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jjohnson
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diff changeset
98 'rawSpectraMaxDynamicRange',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
99 'minimumNumAAToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
100 'minimumNumPeaksToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
101 'skipRawAnnotation',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
102 'minimumDeltaCnToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
103 'maximumMassDiffToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
104 'bracketSpectra',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
105 'mergeBracket',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
106 'filterCriteria',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
107 'combineAction',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
108 'buildAction',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
109 'refreshDatabase',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
110 'reduceSpectra',
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jjohnson
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diff changeset
111 'refreshDeleteUnmapped',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
112 'refreshDeleteMultimapped',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
113 'reannotatePeaks',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
114 'minimumMRMQ3MZ',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
115 'maximumMRMQ3MZ',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
116 'refreshTrypticOnly',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
117 'minimumNumReplicates',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
118 'removeDissimilarReplicates',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
119 'peakQuorum',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
120 'maximumNumPeaksUsed',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
121 'maximumNumReplicates',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
122 'maximumNumPeaksKept',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
123 'replicateWeight',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
124 'recordRawSpectra',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
125 'minimumNumReplicates',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
126 'qualityLevelRemove,',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
127 'qualityPenalizeSingletons',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
128 'qualityImmuneProbThreshold',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
129 'qualityImmuneMultipleEngines',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
130 'useBayesianDenoiser',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
131 'trainBayesianDenoiser',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
132 'denoiserMinimumSignalProb',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
133 'denoiserParamFile',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
134 'decoyConcatenate',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
135 'decoySizeRatio',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
136 'decoyPrecursorSwap',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
137 'normalizeRTWithLandmarks',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
138 'normalizeRTLinearRegression',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
139 'unidentifiedClusterIndividualRun',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
140 'unidentifiedClusterMinimumDot',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
141 'unidentifiedRemoveSinglyCharged',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
142 'unidentifiedMinimumNumPeaksToInclude',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
143 'unidentifiedSingletonXreaThreshold',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
diff changeset
144 'allowableModTokens'
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
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145 ]
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents: 2
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146
2
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jjohnson
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147 search_opts = [
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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diff changeset
148 'libraryFile',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
149 'databaseFile',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
150 'databaseType',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
151 'indexCacheAll',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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152 # 'filterSelectedListFileName',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
153 'precursorMzTolerance',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
154 'precursorMzUseAverage',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
155 'searchAllCharges',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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156 'detectHomologs',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
157 'fvalFractionDelta',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
158 'useSp4Scoring',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
159 'fvalUseDotBias',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
160 'usePValue',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
diff changeset
161 'useTierwiseOpenModSearch',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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162 # 'expectedCysteineMod',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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163 # 'ignoreSpectraWithUnmodCysteine',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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164 # 'ignoreChargeOneLibSpectra',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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165 # 'ignoreAbnormalSpectra',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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166 'outputExtension',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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167 'outputDirectory',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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168 'hitListTopHitFvalThreshold',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
parents:
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169 'hitListLowerHitsFvalThreshold',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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170 'hitListShowHomologs',
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty
jjohnson
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171 'hitListShowMaxRank',
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172 'hitListOnlyTopHit',
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173 'hitListExcludeNoMatch',
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174 'enzymeForPepXMLOutput',
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175 'printFingerprintingSummary',
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176 'filterMinPeakCount',
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177 'filterAllPeaksBelowMz',
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178 'filterMaxIntensityBelow',
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179 'filterMinMzRange',
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180 'filterCountPeakIntensityThreshold',
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181 'filterRemovePeakIntensityThreshold',
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182 'filterMaxPeaksUsed',
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183 'filterMaxDynamicRange',
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184 'peakScalingMzPower',
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185 'peakScalingIntensityPower',
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186 'peakScalingUnassignedPeaks',
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187 'peakNoBinning',
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188 'peakBinningNumBinsPerMzUnit',
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189 'peakBinningFractionToNeighbor',
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190 'filterLibMaxPeaksUsed',
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191 'filterLightIonsMzThreshold',
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192 'filterITRAQReporterPeaks',
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193 'filterTMTReporterPeaks',
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194 # 'filterRemoveHuge515Threshold',
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195 ]
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196
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197
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198 def __main__():
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199 parser = argparse.ArgumentParser(
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200 description='Parse SpectraST search.params files' +
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201 ' to create an updated search.params')
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202 parser.add_argument(
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203 'param_files', nargs='*',
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204 help='A SpectraST search.params files')
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205 parser.add_argument(
3
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206 '-m', '--mode', choices=['search','create','filter'],
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207 help='')
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208 parser.add_argument(
2
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209 '-o', '--output',
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210 help='Output file (-) for stdout')
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211 args = parser.parse_args()
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212
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213 output_wtr = open(args.output, 'w')\
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214 if args.output and args.output != '-' else sys.stdout
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215
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216 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')
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217
3
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218 valid_opts = search_opts if args.mode == 'search' else create_opts if args.mode == 'create' else filter_opts
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219 valid_params = dict()
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220
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221 # Collect all valid_params
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222 def parse_params(param_file, fh, valid_opts):
2
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223 for i, line in enumerate(fh):
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224 try:
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225 m = optpat.match(line.rstrip())
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226 if m:
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227 k, v = m.groups()
3
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228 if k in valid_opts:
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229 valid_params[k] = v
2
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230 except Exception, e:
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231 print('%s(%d): %s %s' % (param_file, i, line, e),
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232 file=sys.stderr)
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233
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234 if args.param_files:
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235 for param_file in args.param_files:
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236 try:
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237 with open(param_file, 'r') as fh:
3
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238 parse_params(param_file, fh, valid_opts)
2
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239 except Exception, e:
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240 print('parse_params: %s' % e, file=sys.stderr)
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241 else:
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242 try:
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243 parse_params('stdin', sys.stdin)
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244 except Exception, e:
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245 print('parse_params: %s' % e, file=sys.stderr)
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246
3
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247 # Write valid_params
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248 for valid_opt in valid_opts:
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249 if valid_opt in valid_params:
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250 print('%s = %s' % (valid_opt, valid_params[valid_opt]), file=output_wtr)
2
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251
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252
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253 if __name__ == "__main__":
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254 __main__()
3
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255