Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.5 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.4 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.4 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.2 |
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0 |
deseq2 |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
bioconductor-deseq2 | 1.22.1 | package |
bioconductor-rhdf5 | 2.26.2 | package |
bioconductor-tximport | 1.10.0 | package |
bioconductor-genomicfeatures | 1.34.1 | package |
r-getopt | 1.20.2 | package |
r-ggrepel | 0.8.0 | package |
r-gplots | 3.0.1 | package |
r-pheatmap | 1.0.10 | package |
r-rjson | 0.2.20 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts'] output_options|output_selector: ['normCounts', 'normRLog', 'normVST'] |
name: value name: value name: value 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 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts'] batch_factors: batch_factors.tab output_options|output_selector: normCounts |
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 batch_factors.tab value |
Test-3 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts.noheader', 'GSM461180_treat_paired.counts.noheader', 'GSM461181_treat_paired.counts.noheader'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|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 output_options|output_selector: ['normCounts', 'normRLog', 'normVST'] |
name: value name: value name: value 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-4 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab'] tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport output_options|output_selector: |
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-5 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab'] tximport|txtype: sailfish tximport|mapping_format|gtf_file: GRCh38_latest_genomic.gff tximport|mapping_format|mapping_format_selector: gtf tximport|tximport_selector: tximport output_options|output_selector: |
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 GRCh38_latest_genomic.gff value |
Test-6 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish_ensembl/sailfish_quant.sf1.tab', 'sailfish_ensembl/sailfish_quant.sf2.tab', 'sailfish_ensembl/sailfish_quant.sf3.tab'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish_ensembl/sailfish_quant.sf4.tab', 'sailfish_ensembl/sailfish_quant.sf5.tab', 'sailfish_ensembl/sailfish_quant.sf6.tab'] tximport|txtype: sailfish tximport|mapping_format|gtf_file: Homo_sapiens.GRCh38.94.gtf tximport|mapping_format|mapping_format_selector: gtf tximport|tximport_selector: tximport output_options|output_selector: |
name: value |
sailfish_ensembl/sailfish_quant.sf1.tab sailfish_ensembl/sailfish_quant.sf2.tab sailfish_ensembl/sailfish_quant.sf3.tab sailfish_ensembl/sailfish_quant.sf4.tab sailfish_ensembl/sailfish_quant.sf5.tab sailfish_ensembl/sailfish_quant.sf6.tab Homo_sapiens.GRCh38.94.gtf value |
Test-7 |
select_data|countsFile: list collection select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|groups: primary:treated select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|groups: primary:untreated select_data|how: group_tags tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport output_options|output_selector: |
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-8 |
select_data|countsFile: list collection select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|groups: primary:treated select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|groups: primary:untreated select_data|how: group_tags tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport output_options|output_selector: many_contrasts |
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 |
|
Test-9 |
select_data|rep_factorName_0|factorName: Treatment select_data|rep_factorName_0|rep_factorLevel_0|factorLevel: Treated select_data|rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish_ensembl/sailfish_quant.sf1.tab', 'sailfish_ensembl/sailfish_quant.sf2.tab', 'sailfish_ensembl/sailfish_quant.sf3.tab'] select_data|rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated select_data|rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish_ensembl/sailfish_quant.sf4.tab', 'sailfish_ensembl/sailfish_quant.sf5.tab', 'sailfish_ensembl/sailfish_quant.sf6.tab'] tximport|txtype: sailfish tximport|mapping_format|gtf_file: Homo_sapiens.GRCh38.94.gtf tximport|mapping_format|mapping_format_selector: gtf tximport|tximport_selector: tximport output_options|output_selector: output_options|alpha_ma: 0.05 |
name: value |
sailfish_ensembl/sailfish_quant.sf1.tab sailfish_ensembl/sailfish_quant.sf2.tab sailfish_ensembl/sailfish_quant.sf3.tab sailfish_ensembl/sailfish_quant.sf4.tab sailfish_ensembl/sailfish_quant.sf5.tab sailfish_ensembl/sailfish_quant.sf6.tab Homo_sapiens.GRCh38.94.gtf value |