Revision: 31:9a882d108833

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Miscellaneous

Name: DESeq2

Description: Determines differentially expressed features from count tables

Id: deseq2

Guid: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0

Version: 2.11.40.8+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(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)

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toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy1

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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)

Requirements:

name	version	type
bioconductor-deseq2	1.40.2	package
bioconductor-rhdf5	2.44.0	package
bioconductor-tximport	1.28.0	package
bioconductor-genomicfeatures	1.52.1	package
r-getopt	1.20.3	package
r-ggrepel	0.9.3	package
r-gplots	3.1.3	package
r-pheatmap	1.0.12	package
r-rjson	0.2.21	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'] advanced_options|use_beta_priors: True 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 advanced_options|use_beta_priors: True 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', '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 advanced_options|use_beta_priors: False 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-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: ['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 advanced_options|use_beta_priors: True 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-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|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport advanced_options|use_beta_priors: True 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-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/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 advanced_options|use_beta_priors: True 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-7	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 advanced_options|use_beta_priors: True 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-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 advanced_options|use_beta_priors: True 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-9	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 advanced_options|use_beta_priors: True 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-10	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 advanced_options|use_beta_priors: True 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
Test-11	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: sizefactors 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
Test-12	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 advanced_options|esf_cond|size_factor_input: size_factors_out.tsv advanced_options|esf_cond|esf: user advanced_options|use_beta_priors: True 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 size_factors_out.tsv value
Test-13	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: sizefactors 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
Test-14	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'] advanced_options|prefilter_conditional|prefilter_value: 10 advanced_options|prefilter_conditional|prefilter: -P output_options|output_selector: normCounts	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