diff test-data/out_config2.txt @ 0:60573349e9ae draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_config2.txt	Wed Nov 11 21:54:51 2020 +0000
@@ -0,0 +1,100 @@
+[Reads]
+minReadLength = 10000
+desiredCoverage = 0
+noCache = False
+palindromicReads.skipFlagging = False
+palindromicReads.maxSkip = 100
+palindromicReads.maxDrift = 100
+palindromicReads.maxMarkerFrequency = 10
+palindromicReads.alignedFractionThreshold = 0.1
+palindromicReads.nearDiagonalFractionThreshold = 0.1
+palindromicReads.deltaThreshold = 100
+
+[Kmers]
+generationMethod = 0
+k = 10
+probability = 0.1
+enrichmentThreshold = 100
+file = 
+
+[MinHash]
+version = 0
+m = 4
+hashFraction = 0.01
+minHashIterationCount = 10
+alignmentCandidatesPerRead = 20
+minBucketSize = 5
+maxBucketSize = 30
+minFrequency = 5
+allPairs = False
+
+[Align]
+alignMethod = 3
+maxSkip = 30
+maxDrift = 30
+maxTrim = 30
+maxMarkerFrequency = 10
+minAlignedMarkerCount = 100
+minAlignedFraction = 0.4
+matchScore = 6
+mismatchScore = -1
+gapScore = -1
+downsamplingFactor = 0.1
+bandExtend = 10
+maxBand = 1000
+sameChannelReadAlignment.suppressDeltaThreshold = 0
+suppressContainments = False
+
+[ReadGraph]
+creationMethod = 0
+maxAlignmentCount = 6
+minComponentSize = 100
+maxChimericReadDistance = 2
+crossStrandMaxDistance = 6
+containedNeighborCount = 6
+uncontainedNeighborCountPerDirection = 3
+removeConflicts = False
+markerCountPercentile = 0.015
+alignedFractionPercentile = 0.12
+maxSkipPercentile = 0.12
+maxDriftPercentile = 0.12
+maxTrimPercentile = 0.015
+
+[MarkerGraph]
+minCoverage = 10
+maxCoverage = 100
+minCoveragePerStrand = 0
+lowCoverageThreshold = 0
+highCoverageThreshold = 256
+maxDistance = 30
+edgeMarkerSkipThreshold = 100
+pruneIterationCount = 6
+simplifyMaxLength = 10,100,1000
+crossEdgeCoverageThreshold = 0
+refineThreshold = 0
+reverseTransitiveReduction = False
+peakFinder.minAreaFraction = 0.08
+peakFinder.areaStartIndex = 2
+
+[Assembly]
+crossEdgeCoverageThreshold = 3
+markerGraphEdgeLengthThresholdForConsensus = 1000
+consensusCaller = Bayesian:guppy-3.0.5-a
+storeCoverageData = False
+storeCoverageDataCsvLengthThreshold = 0
+writeReadsByAssembledSegment = False
+detangleMethod = 0
+detangle.diagonalReadCountMin = 1
+detangle.offDiagonalReadCountMax = 2
+detangle.offDiagonalRatio = 0.3
+iterative = False
+iterative.iterationCount = 3
+iterative.pseudoPathAlignMatchScore = 1
+iterative.pseudoPathAlignMismatchScore = -1
+iterative.pseudoPathAlignGapScore = -1
+iterative.mismatchSquareFactor = 3
+iterative.minScore = 0
+iterative.maxAlignmentCount = 6
+iterative.bridgeRemovalIterationCount = 3
+iterative.bridgeRemovalMaxDistance = 2
+