| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2 (this tool) |
| bwa_color_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 paired|input1: bwa_wrapper_in4.fastqcssanger genomeSource|refGenomeSource: history genomeSource|ownFile: hg19chrX_midpart.fasta paired|sPaired: single suppressHeader: False |
output: bwa_wrapper_out4.sam |
hg19chrX_midpart.fasta bwa_wrapper_in4.fastqcssanger bwa_wrapper_out4.sam |
| Test-2 |
params|source_select: pre_set genomeSource|indices: equCab2chrM paired|input1: bwa_wrapper_in5.fastqcssanger paired|input2: bwa_wrapper_in6.fastqcssanger genomeSource|refGenomeSource: indexed paired|sPaired: paired suppressHeader: True |
output: bwa_wrapper_out5.sam |
bwa_wrapper_in5.fastqcssanger bwa_wrapper_in6.fastqcssanger bwa_wrapper_out5.sam |
| Test-3 |
params|maxInsertSize: 500 params|gapOpenPenalty: 11 params|readGroup|rglb: lib-child-1-A paired|input1: bwa_wrapper_in4.fastqcssanger params|outputTopN: 3 params|outputTopNDisc: 10 params|readGroup|rgsm: child-1 params|noIterSearch: True params|disallowIndel: 5 params|readGroup|rgfo: params|suboptAlign: params|maxOccurPairing: 100000 genomeSource|indices: hg19chrX_midpart params|fracMissingAligns: 0.04 params|readGroup|specReadGroup: yes params|maxEditDistSeed: 2 params|readGroup|rgds: description params|readGroup|rgdt: 2011-03-14 params|gapExtensPenalty: 4 params|maxGapExtens: -1 params|source_select: full params|seed: -1 params|maxEditDist: 0 params|readGroup|rgpg: params|mismatchPenalty: 3 params|maxGapOpens: 1 params|readGroup|rgks: params|readGroup|rgpl: SOLID params|readGroup|rgid: 474747 params|readGroup|rgpi: 200 params|readGroup|rgcn: suppressHeader: False genomeSource|refGenomeSource: indexed paired|sPaired: single params|readGroup|rgpu: params|disallowLongDel: 16 |
output: bwa_wrapper_out6.sam |
bwa_wrapper_in4.fastqcssanger bwa_wrapper_out6.sam |
| Test-4 |
params|maxGapExtens: -1 params|gapOpenPenalty: 11 params|maxGapOpens: 1 paired|input1: bwa_wrapper_in5.fastqcssanger paired|input2: bwa_wrapper_in6.fastqcssanger params|outputTopN: 3 params|outputTopNDisc: 10 params|maxEditDist: 0 genomeSource|ownFile: chr_m.fasta params|noIterSearch: True params|disallowIndel: 5 suppressHeader: False params|maxInsertSize: 100 params|suboptAlign: params|maxOccurPairing: 2 params|mismatchPenalty: 3 params|fracMissingAligns: 0.04 params|seed: -1 genomeSource|refGenomeSource: history params|readGroup|specReadGroup: no params|maxEditDistSeed: 2 params|source_select: full paired|sPaired: paired params|disallowLongDel: 16 params|gapExtensPenalty: 4 |
output: bwa_wrapper_out7.sam |
chr_m.fasta bwa_wrapper_in5.fastqcssanger bwa_wrapper_in6.fastqcssanger bwa_wrapper_out7.sam |