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goseq tool metadata

Miscellaneous

Name: goseq

Description: tests for overrepresented gene categories

Id: goseq

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

Version: 1.30.1

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/1.32.0

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1 (this tool)

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

r-optparse

1.6.0

package

bioconductor-goseq

1.30.0

package

bioconductor-org.hs.eg.db

3.5.0

package

bioconductor-org.dm.eg.db

3.5.0

package

bioconductor-org.dr.eg.db

3.5.0

package

bioconductor-org.mm.eg.db

3.5.0

package

r-dplyr

0.7.6

package

r-ggplot2

3.0.0

package

Functional tests

name

inputs

outputs

required files

Test-1

categorySource|catSource: history
categorySource|category_file: category.tab
out|topgo_plot: True
length_file: gene_length.tab
adv|use_genes_without_cat: True
dge_file: dge_list.tab

attributes: name

dge_list.tab
gene_length.tab
category.tab
name

Test-2

categorySource|catSource: history
adv|use_genes_without_cat: True
length_file: gene_length.tab
dge_file: dge_list.tab
categorySource|category_file: category.tab

attributes: name

dge_list.tab
gene_length.tab
category.tab
name

Test-3

categorySource|catSource: getgo
categorySource|gene_id: ensGene
length_file: gene_length.tab
adv|use_genes_without_cat: True
categorySource|genome: hg38
dge_file: dge_list.tab

attributes: name

dge_list.tab
gene_length.tab
name

Test-4

categorySource|catSource: getgo
categorySource|gene_id: ensGene
length_file: gene_length_zf.tab
adv|use_genes_without_cat: True
categorySource|genome: danRer10
dge_file: dge_list_zf.tab

attributes: name

dge_list_zf.tab
gene_length_zf.tab
name

Test-5

categorySource|catSource: history
categorySource|category_file: category.tab
length_file: gene_length.tab
adv|use_genes_without_cat: True
out|make_plots: True
dge_file: dge_list.tab

attributes: name

dge_list.tab
gene_length.tab
category.tab
name

Test-6

categorySource|catSource: history
categorySource|category_file: category.tab
length_file: gene_length.tab
adv|use_genes_without_cat: True
methods|hypergeometric: True
dge_file: dge_list.tab

attributes: name

dge_list.tab
gene_length.tab
category.tab
name

Test-7

attributes: name
attributes: name
attributes: name

dge_list.tab
gene_length.tab
category.tab
name

Test-8

categorySource|catSource: history
categorySource|category_file: category.tab
out|rdata_out: True
length_file: gene_length.tab
adv|use_genes_without_cat: True
dge_file: dge_list.tab

attributes: name

dge_list.tab
gene_length.tab
category.tab
name