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plotDEXSeq tool metadata

Miscellaneous

Name: plotDEXSeq

Description: Visualization of the per gene DEXSeq results

Id: plotdexseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.48.0+galaxy1

Version: 1.48.0+galaxy1

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/plotdexseq/1.48.0+galaxy1 (this tool)

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

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)

Requirements:

name

version

type

bioconductor-dexseq

1.48.0

package

r-getopt

1.20.4

package

r-rjson

0.2.21

package

Additional information about this tool

Command:

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
    #if $pl_width:
    -w $pl_width
    #end if
    #if $pl_height:
    -h $pl_height
    #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

rdata: dexseq.rds
primaryfactor: condition
genes|geneid: FBgn0000053
genes|genes_select: single
fdr_cutoff: 1

name: value

dexseq.rds
value

Test-2

rdata: dexseq.rds
primaryfactor: condition
genes|genefile: plotdexseq_genes.tab
genes|genes_select: list
fdr_cutoff: 1

name: value

dexseq.rds
plotdexseq_genes.tab
value

Test-3

rdata: dexseq.rds
primaryfactor: condition
genes|genefile: plotdexseq_genes.tab
genes|genes_select: list
fdr_cutoff: 1
pl_width: 5
pl_height: 3

name: value

dexseq.rds
plotdexseq_genes.tab
value