Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.48.0+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0 |
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) |
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 |
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
Functional tests |
name | inputs | outputs | required files |
Test-1 |
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'] report: False fdr_cutoff: 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 |
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'] report: False rds: True fdr_cutoff: 0.05 |
name: value name: value |
dexseq.gtf treated1fb.txt treated2fb.txt treated3fb.txt untreated1fb.txt untreated2fb.txt untreated3fb.txt untreated4fb.txt value |