Mercurial > repos > computational-metabolomics > mspurity_purityx
changeset 10:13034c3886f2 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5
| author | computational-metabolomics |
|---|---|
| date | Fri, 13 Sep 2024 12:24:27 +0000 |
| parents | 374022b7b469 |
| children | d84cc9960035 |
| files | README.rst purityA.R purityX.R purityX.xml |
| diffstat | 4 files changed, 11 insertions(+), 12 deletions(-) [+] |
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--- a/README.rst Thu Jun 13 11:36:53 2024 +0000 +++ b/README.rst Fri Sep 13 12:24:27 2024 +0000 @@ -3,13 +3,13 @@ |Git| |Bioconda| |License| -Version v1.28.0+galaxy0 +Version v1.28.0+galaxy1 ------------------------ - msPurity - bioconductor-mspurity v1.28.0 - Galaxy tools - - v0 + - v1 About ------ @@ -52,6 +52,10 @@ Changes ------------------------- +v1.28.0-galaxy1 + - Further fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) + - Fix for purityA file naming (https://github.com/computational-metabolomics/mspurity-galaxy/issues/56) + v1.28.0-galaxy0 - Version bump to v1.28.0 - createMSP now uses the median precursor MZ and precursor RT in the MSP files
--- a/purityA.R Thu Jun 13 11:36:53 2024 +0000 +++ b/purityA.R Fri Sep 13 12:24:27 2024 +0000 @@ -124,7 +124,7 @@ print(pa) save(pa, file = file.path(opt$out_dir, "purityA_output.RData")) -pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)]) +pa@puritydf$filename <- sapply(as.character(pa@puritydf$fileid), function(x) names(pa@fileList)[as.integer(x)]) print(head(pa@puritydf)) write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")
--- a/purityX.R Thu Jun 13 11:36:53 2024 +0000 +++ b/purityX.R Fri Sep 13 12:24:27 2024 +0000 @@ -16,7 +16,6 @@ make_option("--singleFile", default = 0), make_option("--cores", default = 4), make_option("--xgroups", type = "character"), - make_option("--rdata_name", default = "xset"), make_option("--camera_xcms", default = "xset"), make_option("--files", type = "character"), make_option("--galaxy_files", type = "character"), @@ -63,10 +62,10 @@ rtraw_columns <- TRUE } -loadRData <- function(rdata_path, xset_name) { +loadRData <- function(rdata_path, xnames) { # loads an RData file, and returns the named xset object if it is there load(rdata_path) - return(get(ls()[ls() == xset_name])) + return(get(ls()[ls() %in% xnames])) } @@ -90,7 +89,7 @@ } } -target_obj <- loadRData(opt$xset_path, opt$rdata_name) +target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata')) if (opt$camera_xcms == "camera") { xset <- target_obj@xcmsSet
--- a/purityX.xml Thu Jun 13 11:36:53 2024 +0000 +++ b/purityX.xml Fri Sep 13 12:24:27 2024 +0000 @@ -18,11 +18,7 @@ --xgroups='$xgroups.xgroups_value' #end if --camera_xcms=$camera_xcms - #if $camera_xcms == "camera" - --rdata_name=xa - #else - --rdata_name=xset - #end if + --iwNorm=$iw_norm --ilim=$ilim #if $isotopes.isotopes == "exclude_default"