# 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 @@
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@@ -102,6 +99,20 @@
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