# HG changeset patch # User lecorguille # Date 1541795628 18000 # Node ID 3385de0c090871094f5a22ac6619b8388ddc2154 # Parent a589c4409f7ce9bc5387c94333c0e3045f112b37 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 diff -r a589c4409f7c -r 3385de0c0908 lib.r --- a/lib.r Thu Oct 04 09:51:25 2018 -0400 +++ b/lib.r Fri Nov 09 15:33:48 2018 -0500 @@ -198,6 +198,9 @@ variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) + # FIX: issue when the vector at peakidx is too long and is written in a new line during the export + variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") + write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) @@ -260,9 +263,9 @@ #Create the sampleMetada dataframe sampleMetadata <- xdata@phenoData@data rownames(sampleMetadata) <- NULL - colnames(sampleMetadata) <- c("sampleMetadata", "class") + colnames(sampleMetadata) <- c("sample_name", "class") - sampleNamesOrigin <- sampleMetadata$sampleMetadata + sampleNamesOrigin <- sampleMetadata$sample_name sampleNamesMakeNames <- make.names(sampleNamesOrigin) if (any(duplicated(sampleNamesMakeNames))) { @@ -280,7 +283,7 @@ } } - sampleMetadata$sampleMetadata <- sampleNamesMakeNames + sampleMetadata$sample_name <- sampleNamesMakeNames #For each sample file, the following actions are done diff -r a589c4409f7c -r 3385de0c0908 macros_xcms.xml --- a/macros_xcms.xml Thu Oct 04 09:51:25 2018 -0400 +++ b/macros_xcms.xml Fri Nov 09 15:33:48 2018 -0500 @@ -90,9 +90,6 @@ - - - @@ -102,6 +99,20 @@ + + + +
+ + +
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+ + + + + +