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DISCO tool metadata

Miscellaneous

Name: DISCO

Description: to assemble metagenomics data using an overlap-layout-consensus (OLC) approach

Id: disco

Guid: toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0

Version: 1.2.0

Version command string: runDisco.sh --version

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.1

toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0 (this tool)

disco

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

disco

1.2

package

Functional tests

name

inputs

outputs

required files

Test-1

third_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
second_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
second_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minUniquePEsupport: 3
third_assembly_iter_param|minUniquePEsupport: 3
second_assembly_iter_param|minReadsCountToHave0Flow: 15
second_assembly_iter_param|minOverlapDifference4ClipBranches: 25
first_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
input|library_type: paired
input|paired_input|in2: ecoli_1K_2.fq
first_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
third_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
MinOverlap4BuildGraph: 20
osg: False
input|paired_input|type: separated
second_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
first_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minSequenceLengthTobePrinted: 1000
third_assembly_iter_param|minReadsCountToHave0Flow: 15
second_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
third_assembly_iter_param|minOverlapDifference4ClipBranches: 25
third_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
third_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
second_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
second_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
first_assembly_iter_param|minOverlapDifference4ClipBranches: 25
third_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
first_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minSequenceLengthTobePrinted: 1000
PrintGFA2: True
first_assembly_iter_param|MinOverlap4SimplifyGraph: 30
PrintUnused: True
input|paired_input|in1: ecoli_1K_1.fq
third_assembly_iter_param|minFoldToBeShortBranch: 5
log: True
third_assembly_iter_param|MinOverlap4SimplifyGraph: 30
obg: False
PrintGFA: True
second_assembly_iter_param|minUniquePEsupport: 3
second_assembly_iter_param|MinOverlap4SimplifyGraph: 30
third_assembly_iter_param|minSequenceLengthTobePrinted: 1000
third_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
first_assembly_iter_param|minReadsCountToHave0Flow: 15

log: None
contigs: test1_contigs.fasta
scaffolds: test1_scaffolds.fasta

ecoli_1K_1.fq
ecoli_1K_2.fq
test1_contigs.fasta
test1_scaffolds.fasta

Test-2

third_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
second_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
second_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minUniquePEsupport: 3
third_assembly_iter_param|minUniquePEsupport: 3
second_assembly_iter_param|minReadsCountToHave0Flow: 15
second_assembly_iter_param|minOverlapDifference4ClipBranches: 25
first_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
input|library_type: paired
third_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
first_assembly_iter_param|minNonUniquePEsupport: 0
MinOverlap4BuildGraph: 20
third_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
first_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
osg: False
input|paired_input|type: interleaved
second_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
first_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minSequenceLengthTobePrinted: 1000
third_assembly_iter_param|minReadsCountToHave0Flow: 15
second_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
third_assembly_iter_param|minOverlapDifference4ClipBranches: 25
input|paired_input|inP: ['ecoli_1K_interleaved.fq', 'ecoli_1K_interleaved.fq']
third_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
third_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
second_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
first_assembly_iter_param|minOverlapDifference4ClipBranches: 25
first_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minSequenceLengthTobePrinted: 1000
PrintGFA2: False
first_assembly_iter_param|MinOverlap4SimplifyGraph: 30
PrintUnused: False
third_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
second_assembly_iter_param|minFoldToBeShortBranch: 5
log: True
third_assembly_iter_param|MinOverlap4SimplifyGraph: 30
obg: False
PrintGFA: False
second_assembly_iter_param|minUniquePEsupport: 3
second_assembly_iter_param|MinOverlap4SimplifyGraph: 30
third_assembly_iter_param|minSequenceLengthTobePrinted: 1000
third_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
first_assembly_iter_param|minReadsCountToHave0Flow: 15

log: None
contigs: test2_contigs.fasta
scaffolds: test2_scaffolds.fasta

ecoli_1K_interleaved.fq
test2_contigs.fasta
test2_scaffolds.fasta

Test-3

third_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
second_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
second_assembly_iter_param|minNonUniquePEsupport: 0
first_assembly_iter_param|minUniquePEsupport: 3
third_assembly_iter_param|minUniquePEsupport: 3
second_assembly_iter_param|minReadsCountToHave0Flow: 15
second_assembly_iter_param|minOverlapDifference4ClipBranches: 25
first_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
input|library_type: single
third_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
first_assembly_iter_param|minNonUniquePEsupport: 0
third_assembly_iter_param|minReadsCountToHave0Flow: 15
third_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minReadsCountInEdgeToBe1MinFlow: 20
MinOverlap4BuildGraph: 20
osg: False
second_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
first_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
first_assembly_iter_param|minSequenceLengthTobePrinted: 1000
second_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
input|inS: ecoli_1K_1.fq
third_assembly_iter_param|minOverlapDifference4ClipBranches: 25
third_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
third_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minEdgeLengthToHave0Flow: 1500
second_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
first_assembly_iter_param|minOverlapDifference4ClipBranches: 25
first_assembly_iter_param|minFoldToBeShortBranch: 5
second_assembly_iter_param|minSequenceLengthTobePrinted: 1000
PrintGFA2: False
first_assembly_iter_param|MinOverlap4SimplifyGraph: 30
PrintUnused: False
third_assembly_iter_param|minEdgeLengthToBe1MinFlow: 2000
second_assembly_iter_param|minFoldToBeShortBranch: 5
log: False
third_assembly_iter_param|MinOverlap4SimplifyGraph: 30
obg: False
PrintGFA: False
second_assembly_iter_param|minUniquePEsupport: 3
first_assembly_iter_param|minEdgeLengthToBeNotDeadEnd: 1000
second_assembly_iter_param|MinOverlap4SimplifyGraph: 30
third_assembly_iter_param|minSequenceLengthTobePrinted: 1000
third_assembly_iter_param|minReadsCountInEdgeToBeNotDeadEnd: 10
first_assembly_iter_param|minReadsCountToHave0Flow: 15

contigs: test3_contigs.fasta
scaffolds: test3_scaffolds.fasta

ecoli_1K_1.fq
test3_contigs.fasta
test3_scaffolds.fasta