Galaxy |

Remove Unwanted Variation tool metadata

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