Mercurial > repos > iuc > limma_voom
changeset 10:e26047c4562d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
| author | iuc |
|---|---|
| date | Fri, 08 Jun 2018 02:20:16 -0400 |
| parents | 4255881bebb1 |
| children | 7e8af58c8052 |
| files | limma_voom.R limma_voom.xml |
| diffstat | 2 files changed, 7 insertions(+), 4 deletions(-) [+] |
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--- a/limma_voom.R Tue Jun 05 04:28:56 2018 -0400 +++ b/limma_voom.R Fri Jun 08 02:20:16 2018 -0400 @@ -808,9 +808,12 @@ linkData <- rbind(linkData, c(linkName, linkAddr)) invisible(dev.off()) - # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene names in 2nd column) + # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene labels/symbols in 2nd column) if (haveAnno) { - Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, groups=factors[, 1], + # make gene labels unique to handle NAs + geneanno <- y$genes + geneanno[, 2] <- make.unique(geneanno[, 2]) + Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1], status=status[, i], sample.cols=col.group, main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], folder=paste0("glimma_", unmake.names(con)), launch=FALSE)
--- a/limma_voom.xml Tue Jun 05 04:28:56 2018 -0400 +++ b/limma_voom.xml Fri Jun 08 02:20:16 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="limma_voom" name="limma" version="3.34.9.5"> +<tool id="limma_voom" name="limma" version="3.34.9.6"> <description> Perform differential expression with limma-voom or limma-trend </description> @@ -210,7 +210,7 @@ <!-- Contrasts --> <repeat name="rep_contrast" title="Contrast" min="1" default="1"> - <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> + <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> <validator type="empty_field" /> <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator> </param>