Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0.0 |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.24.0.0 |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.20.1 |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.0 |
dexseq |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
bioconductor-dexseq | 1.28.1 | package |
r-getopt | 1.20.2 | package |
r-rjson | 0.2.20 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
gtf: dexseq.gtf rep_factorName_0|factorName: condition rep_factorName_0|factorLevel1: knockdown rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt'] rep_factorName_0|factorLevel2: control rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt'] report: False fdr_cutoff: 1 |
name: value |
dexseq.gtf treated1fb.txt treated2fb.txt treated3fb.txt untreated1fb.txt untreated2fb.txt untreated3fb.txt untreated4fb.txt value |
Test-2 |
gtf: dexseq.gtf rep_factorName_0|factorName: Treatment rep_factorName_0|factorLevel1: knockdown rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt'] rep_factorName_0|factorLevel2: control rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt'] report: True fdr_cutoff: 1 |
name: value |
dexseq.gtf treated1fb.txt treated2fb.txt treated3fb.txt untreated1fb.txt untreated2fb.txt untreated3fb.txt untreated4fb.txt value |
Test-3 |
gtf: dexseq.gtf rep_factorName_0|factorName: condition rep_factorName_0|factorLevel1: knockdown rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt'] rep_factorName_0|factorLevel2: control rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt'] rep_factorName_1|factorName: libtype rep_factorName_1|factorLevel1: singleend rep_factorName_1|countFiles1: ['treated1fb.txt', 'untreated1fb.txt', 'untreated2fb.txt'] rep_factorName_1|factorLevel2: pairedend rep_factorName_1|countFiles2: ['treated2fb.txt', 'treated3fb.txt', 'untreated3fb.txt', 'untreated4fb.txt'] report: False fdr_cutoff: 0.05 |
name: value |
dexseq.gtf treated1fb.txt treated2fb.txt treated3fb.txt untreated1fb.txt untreated2fb.txt untreated3fb.txt untreated4fb.txt treated1fb.txt untreated1fb.txt untreated2fb.txt treated2fb.txt treated3fb.txt untreated3fb.txt untreated4fb.txt value |
Test-4 |
gtf: dexseq.gtf rep_factorName_0|factorName: condition rep_factorName_0|factorLevel1: knockdown rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt'] rep_factorName_0|factorLevel2: control rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt'] report: False rds: True fdr_cutoff: 0.05 |
name: value name: value |
dexseq.gtf treated1fb.txt treated2fb.txt treated3fb.txt untreated1fb.txt untreated2fb.txt untreated3fb.txt untreated4fb.txt value |