Mercurial > repos > lecorguille > xcms_retcor
changeset 43:221a8c6de94a draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
| author | lecorguille |
|---|---|
| date | Mon, 29 Apr 2019 06:12:54 -0400 |
| parents | feb216e6aef7 |
| children | db348cb32618 |
| files | README.rst abims_xcms_retcor.xml lib.r macros_xcms.xml xcms_retcor.r |
| diffstat | 5 files changed, 12 insertions(+), 8 deletions(-) [+] |
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--- a/README.rst Fri Feb 08 10:01:19 2019 -0500 +++ b/README.rst Mon Apr 29 06:12:54 2019 -0400 @@ -2,9 +2,11 @@ Changelog/News -------------- -**Version 3.4.3.0 - 08/02/2019** +.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 +**Version 3.4.4.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) **Version 3.0.0.0 - 08/03/2018**
--- a/abims_xcms_retcor.xml Fri Feb 08 10:01:19 2019 -0500 +++ b/abims_xcms_retcor.xml Mon Apr 29 06:12:54 2019 -0400 @@ -306,9 +306,11 @@ Changelog/News -------------- -**Version 3.4.3.0 - 08/02/2019** +.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 +**Version 3.4.4.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) **Version 3.0.0.0 - 08/03/2018**
--- a/lib.r Fri Feb 08 10:01:19 2019 -0500 +++ b/lib.r Mon Apr 29 06:12:54 2019 -0400 @@ -69,7 +69,7 @@ chromBPI_adjusted_merged <- chromBPI_adjusted } else { if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) - else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) + else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") singlefile_merged <- c(singlefile_merged,singlefile) @@ -333,7 +333,7 @@ files[exists] <- sub("//","/",files[exists]) # WHAT IS ON THE FILESYSTEM - filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) + filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] # COMPARISON
--- a/macros_xcms.xml Fri Feb 08 10:01:19 2019 -0500 +++ b/macros_xcms.xml Mon Apr 29 06:12:54 2019 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.4.3</token> + <token name="@WRAPPER_VERSION@">3.4.4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
--- a/xcms_retcor.r Fri Feb 08 10:01:19 2019 -0500 +++ b/xcms_retcor.r Mon Apr 29 06:12:54 2019 -0400 @@ -92,7 +92,7 @@ cat("\n\n") #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted") +objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted") save(list=objects2save[objects2save %in% ls()], file="retcor.RData") cat("\n\n")