Revision: 6:26126538a86f

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

Miscellaneous

Name: MAGeCK mle

Description: - perform maximum-likelihood estimation of gene essentiality scores

Id: mageck_mle

Guid: toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.9.2.1

Version: 0.5.9.2.1

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_mle/mageck_mle/0.5.9.2.1 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.8.1

toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.7.1

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

mageck_mle

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|out_log: True samples|design_matrix: in.mle.design_matrix.txt count_table: demo/demo1/sample.txt	attributes: name attributes: name attributes: name	demo/demo1/sample.txt in.mle.design_matrix.txt name
Test-2	adv|sgrnaeff|sgrnaeff_file_select: yes adv|sgrnaeff|sgrnaeff_file: in.mle.sgrnaeff count_table: demo/demo1/sample.txt samples|design_matrix: in.mle.design_matrix.txt adv|sgrnaeff|sgrnaeff_score_col: 4 adv|sgrnaeff|sgrnaeff_name_col: 2	attributes: name attributes: name	demo/demo1/sample.txt in.mle.design_matrix.txt in.mle.sgrnaeff name