Repository revision
2:96a15cf82c50

Repository 'complex_repository_dependency_on_bwa_059'
hg clone https://testtoolshed.g2.bx.psu.edu/repos/greg/complex_repository_dependency_on_bwa_059

Map with BWA for Illumina tool metadata
Miscellaneous
bwa_wrapper
testtoolshed.g2.bx.psu.edu/repos/greg/complex_repository_dependency_on_bwa_059/bwa_wrapper/1.2.3
1.2.3
None
True
Version lineage of this tool (guids ordered most recent to oldest)
testtoolshed.g2.bx.psu.edu/repos/greg/complex_repository_dependency_on_bwa_059/bwa_wrapper/1.2.3 (this tool)
bwa_wrapper
Requirements (dependencies defined in the <requirements> tag set)
name version type
bwa 0.5.9 package
Functional tests
name inputs outputs required files
Test-1 refGenomeSource: indexed
indices: phiX
sPaired: single
input1: bwa_wrapper_in1.fastqsanger
source_select: pre_set
suppressHeader: true
output: bwa_wrapper_out1.sam
bwa_wrapper_in1.fastqsanger
bwa_wrapper_out1.sam
Test-2 refGenomeSource: history
ownFile: phiX.fasta
sPaired: single
input1: bwa_wrapper_in1.fastqsanger
source_select: full
maxEditDist: 0
fracMissingAligns: 0.04
maxGapOpens: 1
maxGapExtens: -1
disallowLongDel: 16
disallowIndel: 5
seed: -1
maxEditDistSeed: 2
mismatchPenalty: 3
gapOpenPenalty: 11
gapExtensPenalty: 4
suboptAlign:
noIterSearch: true
outputTopN: 3
outputTopNDisc: 10
maxInsertSize: 500
maxOccurPairing: 100000
specReadGroup: no
suppressHeader: true
output: bwa_wrapper_out2.sam
phiX.fasta
bwa_wrapper_in1.fastqsanger
bwa_wrapper_out2.sam
Test-3 refGenomeSource: indexed
indices: phiX
sPaired: paired
input1: bwa_wrapper_in2.fastqsanger
input2: bwa_wrapper_in3.fastqsanger
source_select: full
maxEditDist: 0
fracMissingAligns: 0.04
maxGapOpens: 1
maxGapExtens: -1
disallowLongDel: 16
disallowIndel: 5
seed: -1
maxEditDistSeed: 2
mismatchPenalty: 3
gapOpenPenalty: 11
gapExtensPenalty: 4
suboptAlign:
noIterSearch: true
outputTopN: 3
outputTopNDisc: 10
maxInsertSize: 500
maxOccurPairing: 100000
specReadGroup: yes
rgid: abcdefg
rgcn:
rgds: descrip
rgdt: 2010-11-01
rgfo:
rgks:
rglb: lib-mom-A
rgpg:
rgpi: 400
rgpl: ILLUMINA
rgpu:
rgsm: mom
suppressHeader: false
output: bwa_wrapper_out3.sam
bwa_wrapper_in2.fastqsanger
bwa_wrapper_in3.fastqsanger
bwa_wrapper_out3.sam
Test-4 refGenomeSource: history
ownFile: phiX.fasta
sPaired: paired
input1: bwa_wrapper_in2.fastqsanger
input2: bwa_wrapper_in3.fastqsanger
source_select: preSet
suppressHeader: true
output: bwa_wrapper_out8.sam
phiX.fasta
bwa_wrapper_in2.fastqsanger
bwa_wrapper_in3.fastqsanger
bwa_wrapper_out8.sam