Revision: 2:fed9d0350d72

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

Miscellaneous

Name: Remove Unwanted Variation

Description: from RNA-seq data

Id: ruvseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.16.0+galaxy1

Version: 1.16.0+galaxy1

Version command string: echo $(R --version | grep version | grep -v GNU)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\$otherPkgs\$RUVSeq\$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/ruvseq/ruvseq/1.26.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.16.0+galaxy1 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.16.0

toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0

ruvseq

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

Requirements:

name	version	type
bioconductor-ruvseq	1.16.0	package
bioconductor-deseq2	1.22.1	package
bioconductor-tximport	1.10.0	package
bioconductor-genomicfeatures	1.34.1	package
r-ggrepel	0.8.0	package
r-getopt	1.20.2	package

Functional tests

name	inputs	outputs	required files
Test-1	rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts'] pdf: True	name: value	GSM461179_treat_single.counts GSM461180_treat_paired.counts GSM461181_treat_paired.counts GSM461176_untreat_single.counts GSM461177_untreat_paired.counts GSM461178_untreat_paired.counts GSM461182_untreat_single.counts value
Test-2	rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts.noheader', 'GSM461180_treat_paired.counts.noheader', 'GSM461181_treat_paired.counts.noheader'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts.noheader', 'GSM461177_untreat_paired.counts.noheader', 'GSM461178_untreat_paired.counts.noheader', 'GSM461182_untreat_single.counts.noheader'] header: False pdf: True	name: value	GSM461179_treat_single.counts.noheader GSM461180_treat_paired.counts.noheader GSM461181_treat_paired.counts.noheader GSM461176_untreat_single.counts.noheader GSM461177_untreat_paired.counts.noheader GSM461178_untreat_paired.counts.noheader GSM461182_untreat_single.counts.noheader value
Test-3	rep_factorLevel_0|factorLevel: Treated rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab'] rep_factorLevel_1|factorLevel: Untreated rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab'] min_mean_count: 0 tximport|txtype: sailfish tximport|mapping_format|tabular_file: tx2gene.tab tximport|mapping_format|mapping_format_selector: tabular tximport|tximport_selector: tximport pdf: True	name: value	sailfish/sailfish_quant.sf1.tab sailfish/sailfish_quant.sf2.tab sailfish/sailfish_quant.sf3.tab sailfish/sailfish_quant.sf4.tab sailfish/sailfish_quant.sf5.tab sailfish/sailfish_quant.sf6.tab tx2gene.tab value