Mercurial > repos > iuc > shasta

comparison test-data/out_config.txt @ 0:60573349e9ae draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
author iuc
date Wed, 11 Nov 2020 21:54:51 +0000
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-1:000000000000 0:60573349e9ae
1 [Reads]
2 minReadLength = 10000
3 desiredCoverage = 0
4 noCache = False
5 palindromicReads.skipFlagging = False
6 palindromicReads.maxSkip = 100
7 palindromicReads.maxDrift = 100
8 palindromicReads.maxMarkerFrequency = 10
9 palindromicReads.alignedFractionThreshold = 0.1
10 palindromicReads.nearDiagonalFractionThreshold = 0.1
11 palindromicReads.deltaThreshold = 100
12
13 [Kmers]
14 generationMethod = 0
15 k = 10
16 probability = 0.1
17 enrichmentThreshold = 100
18 file =
19
20 [MinHash]
21 version = 0
22 m = 4
23 hashFraction = 0.01
24 minHashIterationCount = 10
25 alignmentCandidatesPerRead = 20
26 minBucketSize = 5
27 maxBucketSize = 30
28 minFrequency = 5
29 allPairs = False
30
31 [Align]
32 alignMethod = 3
33 maxSkip = 30
34 maxDrift = 30
35 maxTrim = 30
36 maxMarkerFrequency = 10
37 minAlignedMarkerCount = 100
38 minAlignedFraction = 0.4
39 matchScore = 6
40 mismatchScore = -1
41 gapScore = -1
42 downsamplingFactor = 0.1
43 bandExtend = 10
44 maxBand = 1000
45 sameChannelReadAlignment.suppressDeltaThreshold = 0
46 suppressContainments = False
47
48 [ReadGraph]
49 creationMethod = 0
50 maxAlignmentCount = 6
51 minComponentSize = 100
52 maxChimericReadDistance = 2
53 crossStrandMaxDistance = 6
54 containedNeighborCount = 6
55 uncontainedNeighborCountPerDirection = 3
56 removeConflicts = False
57 markerCountPercentile = 0.015
58 alignedFractionPercentile = 0.12
59 maxSkipPercentile = 0.12
60 maxDriftPercentile = 0.12
61 maxTrimPercentile = 0.015
62
63 [MarkerGraph]
64 minCoverage = 10
65 maxCoverage = 100
66 minCoveragePerStrand = 0
67 lowCoverageThreshold = 0
68 highCoverageThreshold = 256
69 maxDistance = 30
70 edgeMarkerSkipThreshold = 100
71 pruneIterationCount = 6
72 simplifyMaxLength = 10,100,1000
73 crossEdgeCoverageThreshold = 0
74 refineThreshold = 0
75 reverseTransitiveReduction = False
76 peakFinder.minAreaFraction = 0.08
77 peakFinder.areaStartIndex = 2
78
79 [Assembly]
80 crossEdgeCoverageThreshold = 3
81 markerGraphEdgeLengthThresholdForConsensus = 1000
82 consensusCaller = Bayesian:guppy-3.0.5-a
83 storeCoverageData = False
84 storeCoverageDataCsvLengthThreshold = 0
85 writeReadsByAssembledSegment = True
86 detangleMethod = 0
87 detangle.diagonalReadCountMin = 1
88 detangle.offDiagonalReadCountMax = 2
89 detangle.offDiagonalRatio = 0.3
90 iterative = False
91 iterative.iterationCount = 3
92 iterative.pseudoPathAlignMatchScore = 1
93 iterative.pseudoPathAlignMismatchScore = -1
94 iterative.pseudoPathAlignGapScore = -1
95 iterative.mismatchSquareFactor = 3
96 iterative.minScore = 0
97 iterative.maxAlignmentCount = 6
98 iterative.bridgeRemovalIterationCount = 3
99 iterative.bridgeRemovalMaxDistance = 2
100