Revision: 14:cfb0595f9842

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

Miscellaneous

Name: Volcano Plot

Description: create a volcano plot

Id: volcanoplot

Guid: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/4.0.0+galaxy0

Version: 4.0.0+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggrepel version" $(R --vanilla --slave -e "library(ggrepel); cat(sessionInfo()\$otherPkgs\$ggrepel\$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: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/4.0.0+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/3.5.2+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/3.3.3+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.4

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.2

toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.1

volcanoplot

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

Requirements:

name	version	type
r-ggplot2	4.0.0	package
r-ggrepel	0.9.6	package
r-dplyr	1.1.4	package

Additional information about this tool

Command:

#if $out_options.rscript_out:
        cp '${volcanoplot_script}' rscript.txt &&
    #end if
    Rscript '${volcanoplot_script}'

Interpreter: None

Forces a history refresh: False

Functional tests

name	inputs	outputs	required files
Test-1	input: input.tab with_header|fdr_col: 4 with_header|pval_col: 3 with_header|lfc_col: 2 with_header|label_col: 1 lfc_thresh: 0	name: value	input.tab value
Test-2	input: input.tab with_header|fdr_col: 4 with_header|pval_col: 3 with_header|lfc_col: 2 with_header|label_col: 1 lfc_thresh: 0 labels|label_file: labels.tab labels|label_select: file	name: value	input.tab labels.tab value
Test-3	input: input.tab with_header|fdr_col: 4 with_header|pval_col: 3 with_header|lfc_col: 2 with_header|label_col: 1 with_header|header: yes lfc_thresh: 0 labels|label_file: labels.tab labels|label_select: file out_options|rscript_out: True	name: value name: value	input.tab labels.tab value
Test-4	input: category.tab with_header|fdr_col: 4 with_header|pval_col: 3 with_header|lfc_col: 2 with_header|label_col: 1 with_header|shape_col: 5 shape_or_facet: facet lfc_thresh: 0 labels|label_file: labels.tab labels|label_select: file	name: value	category.tab labels.tab value
Test-5	input: category.tab with_header|fdr_col: 4 with_header|pval_col: 3 with_header|lfc_col: 2 with_header|label_col: 1 with_header|shape_col: 5 shape_or_facet: shape lfc_thresh: 0 labels|label_file: labels.tab labels|label_select: file	name: value	category.tab labels.tab value