Galaxy |

DEXSeq tool metadata

Miscellaneous

Name: DEXSeq

Description: Determines differential exon usage from count tables

Id: dexseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0

Version: 1.44+galaxy0

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/1.48.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0 (this tool)

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

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)

Requirements:

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

Command:

mkdir ./html_out &&
 #import json
 Rscript '$__tool_directory__/dexseq.R'
     -o '$dexseq_out'
     -p \${GALAXY_SLOTS:-4}
     #set $temp_factor_names = list()
     #for $factor in $rep_factorName:
         #set $temp_factor = list()
         #set $count_files1 = list()
         #for $file in $factor.countFiles1:
             $count_files1.append(str($file))
         #end for
         $temp_factor.append( {str($factor.factorLevel1): $count_files1} )

         #set $count_files2 = list()
         #for $file in $factor.countFiles2:
             $count_files2.append(str($file))
         #end for
         $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
         $temp_factor_names.append([str($factor.factorName), $temp_factor])
     #end for
     -f '#echo json.dumps(temp_factor_names)#'
     -a $gtf
     -c $fdr_cutoff
     -d $rds

     #if $report:
         -r ./html_out
         &&
         mkdir '$htmlreport.extra_files_path'
         &&
         cp ./html_out/testForDEU.html $htmlreport
         &&
         cp -r ./html_out/* '$htmlreport.extra_files_path'
     #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-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

name: value
name: value

dexseq.gtf
treated1fb.txt
treated2fb.txt
treated3fb.txt
untreated1fb.txt
untreated2fb.txt
untreated3fb.txt
untreated4fb.txt
value