Mercurial > repos > iuc > shasta

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

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