Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.26.0+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.26.0+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.16.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.16.0 |
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0 |
ruvseq |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
bioconductor-ruvseq | 1.26.0 | package |
bioconductor-deseq2 | 1.32.0 | package |
bioconductor-tximport | 1.20.0 | package |
bioconductor-genomicfeatures | 1.44.0 | package |
r-ggrepel | 0.9.1 | package |
r-getopt | 1.20.3 | package |
r-reshape2 | 1.4.4 | package |
Additional information about this tool |
#if $tximport.tximport_selector == 'tximport': #if $tximport.mapping_format.mapping_format_selector == 'gtf': ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && #else: ln -s '$tximport.mapping_format.tabular_file' mapping.txt && #end if #end if Rscript '${__tool_directory__}/ruvseq.R' #if $pdf: -p '$plots' #end if --sample_json '$sampleTable' $header --min_k $min_k --max_k $max_k --min_mean_count $min_mean_count #if $tximport.tximport_selector == 'tximport': --txtype $tximport.txtype #if $tximport.mapping_format.mapping_format_selector == 'gtf': --tx2gene mapping.gtf #else: --tx2gene mapping.txt #end if #end if #if $ruv_ncounts == 1: --ruv_ncounts #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts'] pdf: True |
name: value |
GSM461179_treat_single.counts GSM461180_treat_paired.counts GSM461181_treat_paired.counts GSM461176_untreat_single.counts GSM461177_untreat_paired.counts GSM461178_untreat_paired.counts GSM461182_untreat_single.counts value |
Test-2 |
rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts.noheader', 'GSM461180_treat_paired.counts.noheader', 'GSM461181_treat_paired.counts.noheader'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts.noheader', 'GSM461177_untreat_paired.counts.noheader', 'GSM461178_untreat_paired.counts.noheader', 'GSM461182_untreat_single.counts.noheader'] header: False pdf: True |
name: value |
GSM461179_treat_single.counts.noheader GSM461180_treat_paired.counts.noheader GSM461181_treat_paired.counts.noheader GSM461176_untreat_single.counts.noheader GSM461177_untreat_paired.counts.noheader GSM461178_untreat_paired.counts.noheader GSM461182_untreat_single.counts.noheader value |
Test-3 |
rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab'] min_mean_count: 0 tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport pdf: True |
name: value |
sailfish/sailfish_quant.sf1.tab sailfish/sailfish_quant.sf2.tab sailfish/sailfish_quant.sf3.tab sailfish/sailfish_quant.sf4.tab sailfish/sailfish_quant.sf5.tab sailfish/sailfish_quant.sf6.tab tx2gene.tab value |
Test-4 |
rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts'] pdf: True ruv_ncounts: True |
name: value |
GSM461179_treat_single.counts GSM461180_treat_paired.counts GSM461181_treat_paired.counts GSM461176_untreat_single.counts GSM461177_untreat_paired.counts GSM461178_untreat_paired.counts GSM461182_untreat_single.counts value |
Test-5 |
rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab'] min_mean_count: 0 tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport pdf: True ruv_ncounts: True |
name: value |
sailfish/sailfish_quant.sf1.tab sailfish/sailfish_quant.sf2.tab sailfish/sailfish_quant.sf3.tab sailfish/sailfish_quant.sf4.tab sailfish/sailfish_quant.sf5.tab sailfish/sailfish_quant.sf6.tab tx2gene.tab value |