Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.36.5 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.10 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.8 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.6 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.5 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.4 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.3 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.2 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.1 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.6.0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/1.2.0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/1.1.1 |
limma_voom |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
bioconductor-limma | 3.38.3 | package |
bioconductor-edger | 3.24.1 | package |
r-statmod | 1.4.30 | package |
r-scales | 1.0.0 | package |
r-rjson | 0.2.20 | package |
r-getopt | 1.20.2 | package |
r-gplots | 3.0.1 | package |
bioconductor-glimma | 1.10.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
rep_contrast_1|contrast: WT-Mut input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype adv|normalisationOption: TMM rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
attributes: name |
matrix.txt name |
Test-2 |
anno|geneanno: anno.txt anno|annoOpt: yes input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype adv|normalisationOption: TMM rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
matrix.txt anno.txt |
|
Test-3 |
adv|normalisationOption: TMM out|rscript: True input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt out|rdaOption: True input|fact|rep_factor_0|factorName: Genotype rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
attributes: name attributes: name |
matrix.txt name |
Test-4 |
input|fact|rep_factor_0|factorName: Genotype adv|normalisationOption: TMM input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt input|fact|rep_factor_1|factorName: Batch input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3 rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
matrix.txt |
|
Test-5 |
adv|normalisationOption: TMM input|format: matrix input|counts: matrix.txt input|fact|ffile: yes input|fact|finfo: factorinfo.txt adv|topgenes: 6 rep_contrast_0|contrast: Mut-WT |
matrix.txt factorinfo.txt |
|
Test-6 |
f|filt|cformat|cntReq: 10 input|format: matrix f|filt|cformat|format_select: counts input|counts: matrix.txt f|filt|filt_select: yes input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT f|filt|cformat|samples|cntSampleReq: 3 input|fact|rep_factor_0|factorName: Genotype f|filt|cformat|samples|count_select: sample adv|normalisationOption: TMM rep_contrast_0|contrast: Mut-WT out|filtCounts: True out|normCounts: True adv|topgenes: 6 |
attributes: name attributes: name |
matrix.txt name |
Test-7 |
input|rep_factor_0|rep_group_0|groupName: WT input|rep_factor_1|factorName: Batch anno|annoOpt: yes input|rep_factor_1|rep_group_0|groupName: b1 input|rep_factor_1|rep_group_2|groupName: b3 input|rep_factor_0|rep_group_1|groupName: Mut input|rep_factor_0|rep_group_1|countsFile: ['Mut1.counts', 'Mut2.counts', 'Mut3.counts'] anno|geneanno: anno.txt input|rep_factor_0|rep_group_0|countsFile: ['WT1.counts', 'WT2.counts', 'WT3.counts'] input|rep_factor_1|rep_group_0|countsFile: ['WT1.counts', 'Mut1.counts'] rep_contrast_1|contrast: WT-Mut adv|topgenes: 6 input|rep_factor_0|factorName: Genotype out|normCounts: True rep_contrast_0|contrast: Mut-WT input|rep_factor_1|rep_group_2|countsFile: ['WT3.counts', 'Mut3.counts'] input|rep_factor_1|rep_group_1|countsFile: ['WT2.counts', 'Mut2.counts'] input|rep_factor_1|rep_group_1|groupName: b2 input|format: files |
attributes: name |
WT1.counts WT2.counts WT3.counts Mut1.counts Mut2.counts Mut3.counts WT1.counts Mut1.counts WT2.counts Mut2.counts WT3.counts Mut3.counts anno.txt name |
Test-8 |
deMethod|de_select: trend adv|normalisationOption: TMM input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt out|rdaOption: True input|fact|rep_factor_0|factorName: Genotype rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
attributes: name |
matrix.txt name |
Test-9 |
deMethod|de_select: trend anno|geneanno: anno.txt anno|annoOpt: yes input|format: matrix input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|counts: matrix.txt out|rdaOption: True input|fact|rep_factor_0|factorName: Genotype adv|normalisationOption: TMM rep_contrast_0|contrast: Mut-WT adv|topgenes: 6 |
attributes: name |
matrix.txt anno.txt name |