Mercurial > repos > ethevenot > checkformat
diff checkformat_wrapper.R @ 3:80a38d36f946 draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
author | ethevenot |
---|---|
date | Thu, 11 Jan 2018 10:24:56 -0500 |
parents | b6a6b4cc932a |
children |
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--- a/checkformat_wrapper.R Tue Jun 06 11:51:33 2017 -0400 +++ b/checkformat_wrapper.R Thu Jan 11 10:24:56 2018 -0500 @@ -44,8 +44,8 @@ resLs <- readAndCheckF(argVc["dataMatrix_in"], argVc["sampleMetadata_in"], - argVc["variableMetadata_in"]) -chkL <- resLs[["chkL"]] + argVc["variableMetadata_in"], + as.logical(argVc["makeNameL"])) ##------------------------------ @@ -53,51 +53,77 @@ ##------------------------------ -if(chkL) { +## dataMatrix + +datMN <- resLs[["datMN"]] +datDF <- cbind.data.frame(dataMatrix = colnames(datMN), + as.data.frame(t(datMN))) +write.table(datDF, + file = argVc[["dataMatrix_out"]], + quote = FALSE, + row.names = FALSE, + sep = "\t") - cat("\nTable formats are OK; enjoy your analyses!\n", sep="") +## sampleMetadata - cat("\nEnd of the '", modNamC, "' Galaxy module call: ", - format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") +samDF <- resLs[["samDF"]] +samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), + samDF) +write.table(samDF, + file = argVc["sampleMetadata_out"], + quote = FALSE, + row.names = FALSE, + sep = "\t") - cat("\n\n\n============================================================================") - cat("\nAdditional information about the call:\n") - cat("\n1) Parameters:\n") - print(cbind(value = argVc)) - - cat("\n2) Session Info:\n") - sessioninfo <- sessionInfo() - cat(sessioninfo$R.version$version.string,"\n") - cat("Main packages:\n") - for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") - cat("Other loaded packages:\n") - for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") - - cat("============================================================================\n") - - sink() - -} else { - - cat("\n\n\n============================================================================") - cat("\nAdditional information about the call:\n") - cat("\n1) Parameters:\n") - print(cbind(value = argVc)) - - cat("\n2) Session Info:\n") - sessioninfo <- sessionInfo() - cat(sessioninfo$R.version$version.string,"\n") - cat("Main packages:\n") - for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") - cat("Other loaded packages:\n") - for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") - - cat("============================================================================\n") +## variableMetadata + +varDF <- resLs[["varDF"]] +varDF <- cbind.data.frame(variableMetadata = rownames(varDF), + varDF) +write.table(varDF, + file = argVc["variableMetadata_out"], + quote = FALSE, + row.names = FALSE, + sep = "\t") - sink() - stop("Please check the generated 'information' file") +if(resLs[["chkL"]]) { + + if(resLs[["newL"]]) { + + cat("\nWarning: The sample and/or variable names or orders from the input tables have been modified\n(see the information file for details); please use the new output tables for your analyses.\n") + + } else { + + cat("\nThe input tables have a correct format and can be used for your analyses.\n") + + } } + +cat("\nEnd of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +cat("\n\n\n============================================================================") +cat("\nAdditional information about the call:\n") +cat("\n1) Parameters:\n") +print(cbind(value = argVc)) + +cat("\n2) Session Info:\n") +sessioninfo <- sessionInfo() +cat(sessioninfo$R.version$version.string,"\n") +cat("Main packages:\n") +for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +cat("Other loaded packages:\n") +for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + +cat("============================================================================\n") + +sink() + +if(!resLs[["chkL"]]) { + stop("Please check the generated 'information' file") +} + ## closing ##--------