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Revision: 8:b46e7d48076a

Repository 'bowtie_wrappers'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers

Map with Bowtie for Illumina tool metadata

Miscellaneous

Name: Map with Bowtie for Illumina

Description:

Id: bowtie_wrapper

Guid: toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0

Version: 1.2.0

Version command string: bowtie --version

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 (this tool)

toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.5

toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3

toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2

bowtie_wrapper

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

Requirements:

name

version

type

bowtie

1.2.0

package

Functional tests

name

inputs

outputs

required files

Test-1

singlePaired|sParams|sSettingsType: preSet
singlePaired|sPaired: single
refGenomeSource|index: equCab2chrM
singlePaired|sInput1: bowtie_in2.fastqsanger
suppressHeader: True
refGenomeSource|genomeSource: indexed

output: bowtie_out6.sam

bowtie_in2.fastqsanger
bowtie_out6.sam

Test-2

singlePaired|pMaxInsert: 1000
singlePaired|pParams|pAllValAlignsOption|pValAlign: 1
singlePaired|pParams|pUnmappedFile: True
singlePaired|pInput2: bowtie_in6.fastqsanger
singlePaired|pInput1: bowtie_in5.fastqsanger
singlePaired|pParams|alignModeOption|alignMode: nMode
singlePaired|pParams|pBestOption|pTryHardOption|pTryHard: noTryHard
singlePaired|pParams|pAlignLimit: -1
suppressHeader: True
singlePaired|pParams|pForwardAlign: forward
singlePaired|pParams|alignModeOption|pMismatchQual: 70
refGenomeSource|indexParams|indexSettings: indexPreSet
singlePaired|pParams|pSeed: -1
singlePaired|pParams|pMaxFile: False
singlePaired|pMateOrient: ff
singlePaired|pParams|pSettingsType: full
refGenomeSource|ownFile: phiX.fasta
singlePaired|pParams|pSkip: 0
singlePaired|pParams|pBestOption|pdStrata: noStrata
singlePaired|pParams|pBestOption|pTryHardOption|pdMaxBacktracks: 800
singlePaired|pParams|pSuppressAlign: -1
singlePaired|pParams|pOffrate: -1
singlePaired|pParams|pReverseAlign: reverse
singlePaired|sPaired: paired
singlePaired|pParams|alignModeOption|pMismatchSeed: 2
singlePaired|pParams|pAllValAlignsOption|pAllValAligns: noAllValAligns
singlePaired|pParams|alignModeOption|pSeedLen: 28
singlePaired|pParams|pMinInsert: 0
singlePaired|pParams|pBestOption|pBest: doBest
singlePaired|pParams|pBestOption|pTryHardOption|pMaxAlignAttempt: 100
singlePaired|pParams|pTrimL: 0
refGenomeSource|genomeSource: history
singlePaired|pParams|pTrimH: 0
singlePaired|pParams|alignModeOption|pRounding: round

output: bowtie_out7.sam
output_unmapped_reads_l: bowtie_out8_1.fastq
output_unmapped_reads_r: bowtie_out8_2.fastq

phiX.fasta
bowtie_in5.fastqsanger
bowtie_in6.fastqsanger
bowtie_out7.sam
bowtie_out8_1.fastq
bowtie_out8_2.fastq

Test-3

singlePaired|pMaxInsert: 1000
singlePaired|pParams|pAllValAlignsOption|pValAlign: 1
singlePaired|pParams|pUnmappedFile: True
singlePaired|pInput2: bowtie_in6.fastqillumina
singlePaired|pInput1: bowtie_in5.fastqillumina
singlePaired|pParams|alignModeOption|alignMode: nMode
singlePaired|pParams|pBestOption|pTryHardOption|pTryHard: noTryHard
singlePaired|pParams|pAlignLimit: -1
suppressHeader: True
singlePaired|pParams|pForwardAlign: forward
singlePaired|pParams|alignModeOption|pMismatchQual: 70
refGenomeSource|indexParams|indexSettings: indexPreSet
singlePaired|pParams|pSeed: -1
singlePaired|pParams|pMaxFile: False
singlePaired|pMateOrient: ff
singlePaired|pParams|pSettingsType: full
refGenomeSource|ownFile: phiX.fasta
singlePaired|pParams|pSkip: 0
singlePaired|pParams|pBestOption|pdStrata: noStrata
singlePaired|pParams|pBestOption|pTryHardOption|pdMaxBacktracks: 800
singlePaired|pParams|pSuppressAlign: -1
singlePaired|pParams|pOffrate: -1
singlePaired|pParams|pReverseAlign: reverse
singlePaired|sPaired: paired
singlePaired|pParams|alignModeOption|pMismatchSeed: 2
singlePaired|pParams|pAllValAlignsOption|pAllValAligns: noAllValAligns
singlePaired|pParams|alignModeOption|pSeedLen: 28
singlePaired|pParams|pMinInsert: 0
singlePaired|pParams|pBestOption|pBest: doBest
singlePaired|pParams|pBestOption|pTryHardOption|pMaxAlignAttempt: 100
singlePaired|pParams|pTrimL: 0
refGenomeSource|genomeSource: history
singlePaired|pParams|pTrimH: 0
singlePaired|pParams|alignModeOption|pRounding: round

output: bowtie_out7.sam
output_unmapped_reads_l: bowtie_out8_1.fastqillumina.sorted
output_unmapped_reads_r: bowtie_out8_2.fastqillumina.sorted

phiX.fasta
bowtie_in5.fastqillumina
bowtie_in6.fastqillumina
bowtie_out7.sam
bowtie_out8_1.fastqillumina.sorted
bowtie_out8_2.fastqillumina.sorted

Test-4

singlePaired|pMaxInsert: 1000
singlePaired|pParams|pAllValAlignsOption|pValAlign: 1
singlePaired|pParams|pUnmappedFile: True
singlePaired|pInput2: bowtie_in6.fastqsolexa
singlePaired|pInput1: bowtie_in5.fastqsolexa
singlePaired|pParams|alignModeOption|alignMode: nMode
singlePaired|pParams|pBestOption|pTryHardOption|pTryHard: noTryHard
singlePaired|pParams|pAlignLimit: -1
suppressHeader: True
singlePaired|pParams|pForwardAlign: forward
singlePaired|pParams|alignModeOption|pMismatchQual: 70
refGenomeSource|indexParams|indexSettings: indexPreSet
singlePaired|pParams|pSeed: -1
singlePaired|pParams|pMaxFile: False
singlePaired|pMateOrient: ff
singlePaired|pParams|pSettingsType: full
refGenomeSource|ownFile: phiX.fasta
singlePaired|pParams|pSkip: 0
singlePaired|pParams|pBestOption|pdStrata: noStrata
singlePaired|pParams|pBestOption|pTryHardOption|pdMaxBacktracks: 800
singlePaired|pParams|pSuppressAlign: -1
singlePaired|pParams|pOffrate: -1
singlePaired|pParams|pReverseAlign: reverse
singlePaired|sPaired: paired
singlePaired|pParams|alignModeOption|pMismatchSeed: 2
singlePaired|pParams|pAllValAlignsOption|pAllValAligns: noAllValAligns
singlePaired|pParams|alignModeOption|pSeedLen: 28
singlePaired|pParams|pMinInsert: 0
singlePaired|pParams|pBestOption|pBest: doBest
singlePaired|pParams|pBestOption|pTryHardOption|pMaxAlignAttempt: 100
singlePaired|pParams|pTrimL: 0
refGenomeSource|genomeSource: history
singlePaired|pParams|pTrimH: 0
singlePaired|pParams|alignModeOption|pRounding: round

output: bowtie_out7.sam
output_unmapped_reads_l: bowtie_out8_1.fastqsolexa.sorted
output_unmapped_reads_r: bowtie_out8_2.fastqsolexa.sorted

phiX.fasta
bowtie_in5.fastqsolexa
bowtie_in6.fastqsolexa
bowtie_out7.sam
bowtie_out8_1.fastqsolexa.sorted
bowtie_out8_2.fastqsolexa.sorted

Test-5

singlePaired|sParams|sSuppressAlign: -1
singlePaired|sParams|alignModeOption|sSeedLen: 28
singlePaired|sParams|alignModeOption|sMismatchQual: 70
singlePaired|sParams|sReverseAlign: reverse
singlePaired|sPaired: single
suppressHeader: True
singlePaired|sParams|sAllValAlignsOption|sValAlign: 1
singlePaired|sInput1: bowtie_in2.fastqsanger
singlePaired|sParams|sBestOption|sBest: noBest
singlePaired|sParams|sTrimH: 0
singlePaired|sParams|alignModeOption|sMismatchSeed: 2
singlePaired|sParams|sMaxFile: False
singlePaired|sParams|sTrimL: 0
singlePaired|sParams|sSeed: -1
singlePaired|sParams|sOffrate: -1
singlePaired|sParams|alignModeOption|sRounding: round
singlePaired|sParams|sBestOption|sTryHardOption|sTryHard: doTryHard
singlePaired|sParams|sSettingsType: full
singlePaired|sParams|sUnmappedFile: False
singlePaired|sParams|sSkip: 0
singlePaired|sParams|alignModeOption|alignMode: nMode
refGenomeSource|index: equCab2chrM
singlePaired|sParams|sAllValAlignsOption|sAllValAligns: noAllValAligns
singlePaired|sParams|sForwardAlign: forward
refGenomeSource|genomeSource: indexed
singlePaired|sParams|sAlignLimit: -1

output: bowtie_out9.sam

bowtie_in2.fastqsanger
bowtie_out9.sam

Test-6

refGenomeSource|indexParams|nodc: dc
refGenomeSource|indexParams|offrate: 5
refGenomeSource|indexParams|autoBehavior|autoB: auto
refGenomeSource|indexParams|noref: ref
refGenomeSource|indexParams|ntoa: no
singlePaired|pMaxInsert: 1000
refGenomeSource|indexParams|seed: -1
singlePaired|pInput2: bowtie_in6.fastqsanger
singlePaired|pInput1: bowtie_in5.fastqsanger
singlePaired|sPaired: paired
suppressHeader: True
refGenomeSource|indexParams|indexSettings: indexFull
singlePaired|pParams|pSettingsType: preSet
singlePaired|pMateOrient: ff
refGenomeSource|indexParams|ftab: 10
refGenomeSource|genomeSource: history
refGenomeSource|ownFile: phiX.fasta
refGenomeSource|indexParams|endian: little

output: bowtie_out10.sam

phiX.fasta
bowtie_in5.fastqsanger
bowtie_in6.fastqsanger
bowtie_out10.sam

Test-7

refGenomeSource|indexParams|nodc: dc
refGenomeSource|indexParams|offrate: 5
refGenomeSource|indexParams|autoBehavior|autoB: auto
refGenomeSource|indexParams|noref: ref
refGenomeSource|indexParams|ntoa: no
singlePaired|pMaxInsert: 1000
refGenomeSource|indexParams|seed: -1
singlePaired|pInput2: bowtie_in6.fastqsanger
singlePaired|pInput1: bowtie_in5.fastqsanger
singlePaired|sPaired: paired
suppressHeader: True
refGenomeSource|indexParams|indexSettings: indexFull
singlePaired|pParams|pSettingsType: preSet
singlePaired|pMateOrient: ff
save_mapping_stats: True
refGenomeSource|indexParams|ftab: 10
refGenomeSource|genomeSource: history
refGenomeSource|ownFile: phiX.fasta
refGenomeSource|indexParams|endian: little

output: bowtie_out10.sam
mapping_stats: bowtie_out11.txt

phiX.fasta
bowtie_in5.fastqsanger
bowtie_in6.fastqsanger
bowtie_out10.sam
bowtie_out11.txt