Mercurial > repos > jjohnson > spectrast

annotate spectrast_params.py @ 3:7f02fc51bddf draft

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