Revision: 2:9527a3d6ebd2

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/0.5.7.2

Version: 0.5.7.2

Version command string: echo $(mageck -v )", numpy version" $([python -c "import numpy; numpy.version.version"])", 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/0.5.7.3

toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.2 (this tool)

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	0.5.7	package
numpy	1.14.2	package
r-gplots	3.0.1	package
r-xtable	1.8_2	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	counts: out.count.txt	test1.fastq.gz demo/demo2/library.txt out.count.txt
Test-2	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt out|pdfreportOpt: True reads|sample: ['test1.fastq.gz', 'test2.fastq.gz']	counts: out.count_multi.txt pdfreport: out.countsummary_multi.pdf	test1.fastq.gz test2.fastq.gz demo/demo2/library.txt out.count_multi.txt out.countsummary_multi.pdf
Test-3	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt reads|sample_label: test1_fastq_gz reads|sample: demo/demo2/test1.fastq	counts: out.count.txt	demo/demo2/test1.fastq demo/demo2/library.txt out.count.txt
Test-4	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt reads|sample: test1.bam	counts: out.count.bam.txt	test1.bam demo/demo2/library.txt out.count.bam.txt
Test-5	reads|format_select: files reads|sgrna_library_file: demo/demo2/library.txt out|logOpt: True out|unmappedOpt: True out|pdfreportOpt: True out|rfilesOpt: True out|countsummaryOpt: True reads|sample: test1.fastq.gz	counts: out.count.fastq.txt countsummary: out.countsummary.txt normcounts: output.count_normalized.txt log: out.count.log.txt unmapped: out.count.unmapped.txt pdfreport: out.countsummary.pdf rscript: out.count.R rnwfile: output_countsummary.Rnw	test1.fastq.gz demo/demo2/library.txt out.count.fastq.txt out.countsummary.txt output.count_normalized.txt out.count.log.txt out.count.unmapped.txt out.countsummary.pdf out.count.R output_countsummary.Rnw