Revision: 7:e329d44424d7

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

Miscellaneous

Name: MAGeCK count

Description: - collect sgRNA read counts from read mapping files

Id: mageck_count

Guid: toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4

Version: 0.5.9.2.4

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_count/mageck_count/0.5.9.2.4 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.8.4

toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.4

toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.3

toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.2

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

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

mageck_count

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
ghostscript	9.22	package

Functional tests

name	inputs	outputs	required files
Test-1	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt reads|sample: test1.fastq.gz	attributes: name	test1.fastq.gz demo/demo2/library.txt name
Test-2	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt reads|sample: ['test1.fastq.gz', 'test2.fastq.gz'] out|pdfreportOpt: True	attributes: name attributes: name	test1.fastq.gz test2.fastq.gz demo/demo2/library.txt name
Test-3	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt reads|sample: test1.bam	attributes: name	test1.bam demo/demo2/library.txt name
Test-4	reads|format_select: files out|pdfreportOpt: True out|countsummaryOpt: True reads|sample: test1.fastq.gz reads|sgrna_library_file: demo/demo2/library.txt out|logOpt: True out|unmappedOpt: True out|rfilesOpt: True	attributes: name attributes: name attributes: name attributes: name attributes: name attributes: name attributes: name attributes: name	test1.fastq.gz demo/demo2/library.txt name