Mercurial > repos > lecorguille > msnbase_readmsdata
changeset 4:fd809bde6aec draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
| author | lecorguille |
|---|---|
| date | Fri, 09 Nov 2018 15:09:19 -0500 |
| parents | 11faa3dd548e |
| children | 2a69f9923a70 |
| files | lib.r repository_dependencies.xml test-data/sampleMetadata.tsv |
| diffstat | 3 files changed, 11 insertions(+), 8 deletions(-) [+] |
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--- a/lib.r Thu Oct 04 10:34:33 2018 -0400 +++ b/lib.r Fri Nov 09 15:09:19 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
--- a/repository_dependencies.xml Thu Oct 04 10:34:33 2018 -0400 +++ b/repository_dependencies.xml Fri Nov 09 15:09:19 2018 -0500 @@ -1,5 +1,5 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file