Repository revision
11:602de62d995b

Repository 'goseq'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/goseq

goseq tool metadata
Miscellaneous
goseq
tests for overrepresented gene categories
goseq
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0
1.50.0+galaxy0
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" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.36.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.32.0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/0.2.2
goseq
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-goseq 1.50.0 package
bioconductor-org.hs.eg.db 3.16.0 package
bioconductor-org.dm.eg.db 3.16.0 package
bioconductor-org.dr.eg.db 3.16.0 package
bioconductor-org.mm.eg.db 3.16.0 package
bioconductor-org.rn.eg.db 3.16.0 package
r-dplyr 1.0.10 package
r-ggplot2 3.4.0 package
r-optparse 1.7.3 package
openssl 1.1.1s package
Additional information about this tool
Rscript '$__tool_directory__/goseq.r'

    --dge_file '$dge_file'
    --length_file '$length_file'

#if $categorySource.catSource == 'getgo'
    --genome $categorySource.genome
    --gene_id $categorySource.gene_id
    --fetch_cats '$categorySource.fetchcats'
#elif $categorySource.catSource == 'history'
    --category_file '$categorySource.category_file'
#end if

#if $methods.wallenius
    --wallenius_tab '$wallenius_tab'
#end if
#if $methods.hypergeometric
    --nobias_tab '$nobias_tab'
#end if

    --repcnt $methods.repcnt
#if $methods.repcnt != 0
    --sampling_tab '$sampling_tab'
#end if

    --p_adj_method '$adv.p_adj_method'
    --use_genes_without_cat '$adv.use_genes_without_cat'

#if $out.topgo_plot
    --top_plot '$top_plot'
#end if

#if str($out.make_plots) == 'TRUE'
    --make_plots '$out.make_plots'
    --length_bias_plot '$length_bias_plot'
    #if $methods.repcnt != 0 and $methods.wallenius
    --sample_vs_wallenius_plot '$sample_vs_wallenius_plot'
    #end if
#end if

#if $out.cat_genes
    --categories_genes_out_fp '$cat_genes_tab'
#end if

#if $out.rdata_out
    --rdata '$rdata'
#end if
None
False
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