| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/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 |
params|source_select: pre_set genomeSource|indices: phiX paired|input1: bwa_wrapper_in1.fastqsanger genomeSource|refGenomeSource: indexed paired|sPaired: single suppressHeader: True |
output: bwa_wrapper_out1.sam |
bwa_wrapper_in1.fastqsanger bwa_wrapper_out1.sam |
| Test-2 |
params|maxGapExtens: -1 params|gapOpenPenalty: 11 params|maxGapOpens: 1 paired|input1: bwa_wrapper_in1.fastqsanger params|seed: -1 params|outputTopN: 3 params|outputTopNDisc: 10 genomeSource|ownFile: phiX.fasta params|maxEditDist: 0 params|noIterSearch: True params|disallowIndel: 5 suppressHeader: True params|maxInsertSize: 500 params|suboptAlign: params|maxOccurPairing: 100000 params|mismatchPenalty: 3 params|fracMissingAligns: 0.04 genomeSource|refGenomeSource: history params|readGroup|specReadGroup: no params|maxEditDistSeed: 2 params|source_select: full paired|sPaired: single params|disallowLongDel: 16 params|gapExtensPenalty: 4 |
output: bwa_wrapper_out2.sam |
phiX.fasta bwa_wrapper_in1.fastqsanger bwa_wrapper_out2.sam |
| Test-3 |
params|maxGapExtens: -1 params|gapOpenPenalty: 11 params|readGroup|rglb: lib-mom-A paired|input1: bwa_wrapper_in2.fastqsanger paired|input2: bwa_wrapper_in3.fastqsanger params|outputTopN: 3 params|outputTopNDisc: 10 params|readGroup|rgks: params|readGroup|rgcn: params|maxEditDist: 0 params|readGroup|rgsm: mom params|readGroup|rgpg: params|mismatchPenalty: 3 params|maxGapOpens: 1 params|noIterSearch: True params|disallowIndel: 5 params|readGroup|rgfo: params|readGroup|rgpl: ILLUMINA params|maxInsertSize: 500 params|readGroup|rgpi: 400 params|readGroup|rgid: abcdefg params|suboptAlign: params|maxOccurPairing: 100000 genomeSource|indices: phiX params|fracMissingAligns: 0.04 params|seed: -1 suppressHeader: False genomeSource|refGenomeSource: indexed params|readGroup|specReadGroup: yes params|maxEditDistSeed: 2 params|source_select: full paired|sPaired: paired params|readGroup|rgpu: params|readGroup|rgds: descrip params|disallowLongDel: 16 params|readGroup|rgdt: 2010-11-01 params|gapExtensPenalty: 4 |
output: bwa_wrapper_out3.sam |
bwa_wrapper_in2.fastqsanger bwa_wrapper_in3.fastqsanger bwa_wrapper_out3.sam |
| Test-4 |
paired|input1: bwa_wrapper_in2.fastqsanger paired|input2: bwa_wrapper_in3.fastqsanger genomeSource|refGenomeSource: history genomeSource|ownFile: phiX.fasta paired|sPaired: paired suppressHeader: True |
output: bwa_wrapper_out8.sam |
phiX.fasta bwa_wrapper_in2.fastqsanger bwa_wrapper_in3.fastqsanger bwa_wrapper_out8.sam |