Revision: 6:39a996d44e16

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

Miscellaneous

Name: MAGeCK pathway

Description: - given a ranked gene list, test whether one pathway is enriched

Id: mageck_pathway

Guid: toolshed.g2.bx.psu.edu/repos/iuc/mageck_pathway/mageck_pathway/0.5.9.2

Version: 0.5.9.2

Version command string: echo $(mageck -v )", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", xtable version" $(R --vanilla --slave -e "library(xtable); cat(sessionInfo()\$otherPkgs\$xtable\$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/mageck_pathway/mageck_pathway/0.5.9.2 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/mageck_pathway/mageck_pathway/0.5.8

toolshed.g2.bx.psu.edu/repos/iuc/mageck_pathway/mageck_pathway/0.5.7

mageck_pathway

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

Requirements:

name	version	type
mageck	0.5.9.2	package
r-gplots	3.0.3	package
r-xtable	1.8_4	package
r-ggplot2	3.3.0	package

Functional tests

name	inputs	outputs	required files
Test-1	adv|ranking_column: 2 adv|out_log: True gene_ranking: out.test.gene_summary.txt gmt_file: in.mageckQC.gmt	attributes: name attributes: name	out.test.gene_summary.txt in.mageckQC.gmt name