Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.0+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy2 |
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 |
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 | 3.50.1 | package |
bioconductor-edger | 3.36.0 | package |
r-statmod | 1.4.36 | package |
r-scales | 1.1.1 | package |
r-rjson | 0.2.21 | package |
r-getopt | 1.20.3 | package |
r-gplots | 3.1.1 | package |
bioconductor-glimma | 2.4.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|rep_contrast_1|contrast: WT-Mut cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
name: value |
matrix.txt value |
Test-2 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix anno|geneanno: anno.txt anno|annoOpt: yes cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
matrix.txt anno.txt |
|
Test-3 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no out|rscript: True out|rdaOption: True adv|topgenes: 6 adv|normalisationOption: TMM |
name: value name: value |
matrix.txt value |
Test-4 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|fact|rep_factor_1|factorName: Batch input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3 input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
matrix.txt |
|
Test-5 |
input|counts: matrix.txt input|fact|finfo: factorinfo.txt input|fact|ffile: yes input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
matrix.txt factorinfo.txt |
|
Test-6 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no f|filt|cformat|cntReq: 10 f|filt|cformat|samples|cntSampleReq: 3 f|filt|cformat|samples|count_select: sample f|filt|cformat|format_select: counts f|filt|filt_select: yes out|filtCounts: True out|normCounts: True adv|topgenes: 6 adv|normalisationOption: TMM |
name: value name: value |
matrix.txt value |
Test-7 |
input|rep_factor_0|factorName: Genotype input|rep_factor_0|rep_group_0|groupName: WT input|rep_factor_0|rep_group_0|countsFile: ['WT1.counts', 'WT2.counts', 'WT3.counts'] input|rep_factor_0|rep_group_1|groupName: Mut input|rep_factor_0|rep_group_1|countsFile: ['Mut1.counts', 'Mut2.counts', 'Mut3.counts'] input|rep_factor_1|factorName: Batch input|rep_factor_1|rep_group_0|groupName: b1 input|rep_factor_1|rep_group_0|countsFile: ['WT1.counts', 'Mut1.counts'] input|rep_factor_1|rep_group_1|groupName: b2 input|rep_factor_1|rep_group_1|countsFile: ['WT2.counts', 'Mut2.counts'] input|rep_factor_1|rep_group_2|groupName: b3 input|rep_factor_1|rep_group_2|countsFile: ['WT3.counts', 'Mut3.counts'] input|format: files anno|geneanno: anno.txt anno|annoOpt: yes cont|rep_contrast_0|contrast: Mut-WT cont|rep_contrast_1|contrast: WT-Mut cont|cfile: no out|normCounts: True adv|topgenes: 6 |
name: value |
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 value |
Test-8 |
deMethod|de_select: trend input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
name: value |
matrix.txt value |
Test-9 |
deMethod|de_select: trend input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix anno|geneanno: anno.txt anno|annoOpt: yes cont|rep_contrast_0|contrast: Mut-WT cont|cfile: no adv|topgenes: 6 adv|normalisationOption: TMM |
name: value |
matrix.txt anno.txt value |
Test-10 |
deMethod|de_select: voom input|counts: matrix_num.txt input|fact|rep_factor_0|factorName: Group input|fact|rep_factor_0|groupNames: 2,2,2,1,1,1 input|format: matrix anno|geneanno: anno.txt anno|annoOpt: yes cont|rep_contrast_0|contrast: 2-1 cont|cfile: no f|filt|cformat|cntReq: 10 f|filt|cformat|samples|cntSampleReq: 3 f|filt|cformat|samples|count_select: sample f|filt|cformat|format_select: counts f|filt|filt_select: yes out|normCounts: True adv|topgenes: 6 adv|normalisationOption: TMM |
name: value |
matrix_num.txt anno.txt value |
Test-11 |
input|counts: matrix.txt input|fact|rep_factor_0|factorName: Genotype input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT input|format: matrix cont|cinfo: contrasts.txt cont|cfile: yes adv|topgenes: 6 adv|normalisationOption: TMM |
matrix.txt contrasts.txt |