Repository revision
5:278b189248cd

Repository 'dexseq'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/dexseq

DEXSeq tool metadata
Miscellaneous
DEXSeq
Determines differential exon usage from count tables
dexseq
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0+galaxy1
1.26.0+galaxy1
echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0+galaxy1 (this tool)
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 1.26.0 package
r-getopt 1.20.2 package
r-rjson 0.2.20 package
Functional tests
name inputs outputs required files
Test-1 rep_factorName_0|factorLevel1: knockdown
fdr_cutoff: 1
rep_factorName_0|factorLevel2: control
gtf: dexseq.gtf
rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt']
rep_factorName_0|factorName: condition
report: False
rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt']
attributes: name
dexseq.gtf
treated1fb.txt
treated2fb.txt
treated3fb.txt
untreated1fb.txt
untreated2fb.txt
untreated3fb.txt
untreated4fb.txt
name
Test-2 rep_factorName_0|factorLevel1: knockdown
fdr_cutoff: 1
rep_factorName_0|factorLevel2: control
gtf: dexseq.gtf
rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt']
rep_factorName_0|factorName: Treatment
report: True
rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt']
attributes: name
dexseq.gtf
treated1fb.txt
treated2fb.txt
treated3fb.txt
untreated1fb.txt
untreated2fb.txt
untreated3fb.txt
untreated4fb.txt
name
Test-3 rep_factorName_0|factorLevel1: knockdown
rep_factorName_1|factorLevel2: pairedend
fdr_cutoff: 0.05
rep_factorName_0|factorLevel2: control
rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt']
gtf: dexseq.gtf
rep_factorName_1|factorName: libtype
rep_factorName_1|factorLevel1: singleend
rep_factorName_0|factorName: condition
report: False
rep_factorName_1|countFiles1: ['treated1fb.txt', 'untreated1fb.txt', 'untreated2fb.txt']
rep_factorName_1|countFiles2: ['treated2fb.txt', 'treated3fb.txt', 'untreated3fb.txt', 'untreated4fb.txt']
rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt']
attributes: name
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
name
Test-4 rep_factorName_0|factorLevel1: knockdown
fdr_cutoff: 0.05
rep_factorName_0|factorLevel2: control
rds: True
gtf: dexseq.gtf
report: False
rep_factorName_0|factorName: condition
rep_factorName_0|countFiles1: ['treated1fb.txt', 'treated2fb.txt', 'treated3fb.txt']
rep_factorName_0|countFiles2: ['untreated1fb.txt', 'untreated2fb.txt', 'untreated3fb.txt', 'untreated4fb.txt']
attributes: name
attributes: name
dexseq.gtf
treated1fb.txt
treated2fb.txt
treated3fb.txt
untreated1fb.txt
untreated2fb.txt
untreated3fb.txt
untreated4fb.txt
name