Mercurial > repos > lecorguille > xcms_group
changeset 18:7a19925478e8 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
| author | lecorguille |
|---|---|
| date | Fri, 09 Nov 2018 15:14:35 -0500 |
| parents | 95e689b7f27f |
| children | c8f8d598f562 |
| files | README.rst abims_xcms_group.xml lib.r repository_dependencies.xml |
| diffstat | 4 files changed, 19 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/README.rst Tue Oct 09 04:39:40 2018 -0400 +++ b/README.rst Fri Nov 09 15:14:35 2018 -0500 @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 3.0.0.1 - 09/11/2018** + +- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist + **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
--- a/abims_xcms_group.xml Tue Oct 09 04:39:40 2018 -0400 +++ b/abims_xcms_group.xml Fri Nov 09 15:14:35 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.0"> +<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.1"> <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> @@ -355,6 +355,10 @@ Changelog/News -------------- +**Version 3.0.0.1 - 09/11/2018** + +- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist + **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
--- a/lib.r Tue Oct 09 04:39:40 2018 -0400 +++ b/lib.r Fri Nov 09 15:14:35 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 Tue Oct 09 04:39:40 2018 -0400 +++ b/repository_dependencies.xml Fri Nov 09 15:14:35 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