Mercurial > repos > ethevenot > checkformat
changeset 2:b6a6b4cc932a draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
| author | ethevenot |
|---|---|
| date | Tue, 06 Jun 2017 11:51:33 -0400 |
| parents | e194eec8e70c |
| children | 80a38d36f946 |
| files | checkformat_config.xml checkformat_wrapper.R |
| diffstat | 2 files changed, 35 insertions(+), 7 deletions(-) [+] |
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--- a/checkformat_config.xml Sat Aug 06 11:54:28 2016 -0400 +++ b/checkformat_config.xml Tue Jun 06 11:51:33 2017 -0400 @@ -2,7 +2,6 @@ <description>Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files</description> <requirements> - <requirement type="package" version="3.2.2">R</requirement> <requirement type="package">r-batch</requirement> </requirements> @@ -154,12 +153,11 @@ }</citation> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> - - +<!-- + - --------------- Working example - --------------- + Input files @@ -221,6 +219,6 @@ HMDB01032 Dehydroepiandrosterone sulfate HMDB03072 Quinic acid HMDB00792 Sebacic acid +--> - </tool>
--- a/checkformat_wrapper.R Sat Aug 06 11:54:28 2016 -0400 +++ b/checkformat_wrapper.R Tue Jun 06 11:51:33 2017 -0400 @@ -60,9 +60,39 @@ 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() - + } 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") sink() stop("Please check the generated 'information' file")