Revision: 4:251393b72616

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/dexseq

Miscellaneous

Name: DEXSeq

Description: Determines differential exon usage from count tables

Id: dexseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0.0

Version: 1.26.0.0

Version command string: 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: ")")"

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

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 (this tool)

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)

Requirements:

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