Repository revision
10:df929f257179

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

plotDEXSeq tool metadata
Miscellaneous
plotDEXSeq
Visualization of the per gene DEXSeq results
plotdexseq
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.44+galaxy0
1.44+galaxy0
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/plotdexseq/1.48.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.44+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.28.1.1
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/@VERSION@.1
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.28.1.0
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.26.0.0
plotdexseq
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-dexseq 1.44 package
r-getopt 1.20.3 package
r-rjson 0.2.21 package
Additional information about this tool
Rscript '$__tool_directory__/plotdexseq.R'
    -r '$rdata'
    -p '$primaryfactor'
    #if $genes.genes_select == 'list':
        -f '$genes.genefile'
    #else:
        -g '$genes.geneid'
    #end if
    -c $fdr_cutoff
    -t $transcripts
    -a $names
    -n $normcounts
    -s $splicing
    
None
False
Functional tests
name inputs outputs required files
Test-1 rdata: dexseq.rds
primaryfactor: condition
genes|geneid: FBgn0000053
fdr_cutoff: 1
name: value
dexseq.rds
value
Test-2 rdata: dexseq.rds
primaryfactor: condition
fdr_cutoff: 1
name: value
dexseq.rds
value