Revision: 9:ef2ad746b589

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/goseq

Miscellaneous

Name: goseq

Description: tests for overrepresented gene categories

Id: goseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0

Version: 1.44.0+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\$otherPkgs\$goseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$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/goseq/goseq/1.44.0+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.36.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.32.0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/0.2.2

goseq

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name	version	type
bioconductor-goseq	1.44.0	package
bioconductor-org.hs.eg.db	3.13.0	package
bioconductor-org.dm.eg.db	3.13.0	package
bioconductor-org.dr.eg.db	3.13.0	package
bioconductor-org.mm.eg.db	3.13.0	package
r-dplyr	1.0.6	package
r-ggplot2	3.3.3	package
r-optparse	1.6.6	package

Functional tests

name	inputs	outputs	required files
Test-1	dge_file: dge_list.tab length_file: gene_length.tab categorySource|category_file: category.tab categorySource|catSource: history methods|wallenius: True methods|hypergeometric: False methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: True out|make_plots: False out|cat_genes: False out|rdata_out: False	name: value name: value	dge_list.tab gene_length.tab category.tab value
Test-2	dge_file: dge_list.tab length_file: gene_length.tab categorySource|genome: hg38 categorySource|gene_id: ensGene categorySource|fetchcats: ['GO:CC', 'GO:BP', 'GO:MF'] categorySource|catSource: getgo methods|wallenius: True methods|hypergeometric: False methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: False out|cat_genes: True out|rdata_out: False	name: value name: value	dge_list.tab gene_length.tab value
Test-3	dge_file: dge_list_zf.tab length_file: gene_length_zf.tab categorySource|genome: danRer10 categorySource|gene_id: ensGene categorySource|fetchcats: ['GO:CC', 'GO:BP', 'GO:MF'] categorySource|catSource: getgo methods|wallenius: True methods|hypergeometric: False methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: False out|cat_genes: False out|rdata_out: False	name: value	dge_list_zf.tab gene_length_zf.tab value
Test-4	dge_file: dge_list.tab length_file: gene_length.tab categorySource|category_file: category.tab categorySource|catSource: history methods|wallenius: True methods|hypergeometric: False methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: True out|cat_genes: False out|rdata_out: False	name: value	dge_list.tab gene_length.tab category.tab value
Test-5	dge_file: dge_list.tab length_file: gene_length.tab categorySource|category_file: category.tab categorySource|catSource: history methods|wallenius: True methods|hypergeometric: True methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: False out|cat_genes: False out|rdata_out: False	name: value	dge_list.tab gene_length.tab category.tab value
Test-6	dge_file: dge_list.tab length_file: gene_length.tab categorySource|category_file: category.tab categorySource|catSource: history methods|wallenius: True methods|hypergeometric: False methods|repcnt: 1000 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: True out|cat_genes: False out|rdata_out: False	name: value name: value name: value	dge_list.tab gene_length.tab category.tab value
Test-7	dge_file: dge_list.tab length_file: gene_length.tab categorySource|category_file: category.tab categorySource|catSource: history methods|wallenius: True methods|hypergeometric: False methods|repcnt: 0 adv|p_adj_method: BH adv|use_genes_without_cat: True out|topgo_plot: False out|make_plots: False out|cat_genes: False out|rdata_out: True	name: value	dge_list.tab gene_length.tab category.tab value