Mercurial > repos > computational-metabolomics > mspurity_createmsp
changeset 1:d1d73007a255 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
| author | computational-metabolomics |
|---|---|
| date | Thu, 05 Dec 2019 07:39:41 -0500 |
| parents | 35898942bfbb |
| children | 54593159627d |
| files | flagRemove.R macros.xml purityA.R |
| diffstat | 3 files changed, 18 insertions(+), 10 deletions(-) [+] |
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--- a/flagRemove.R Wed Nov 27 14:20:07 2019 -0500 +++ b/flagRemove.R Thu Dec 05 07:39:41 2019 -0500 @@ -138,7 +138,7 @@ chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] if (length(chosen_blank)>1){ print('ERROR: only 1 blank is currently allowed to be used with this tool') - exit() + quit() } blank_class <- as.character(chosen_blank) print(blank_class) @@ -171,7 +171,7 @@ grp_peaklist <- ffrm_out[[2]] removed_peaks <- ffrm_out[[3]] - save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) + save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'), version=2) # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv')
--- a/macros.xml Wed Nov 27 14:20:07 2019 -0500 +++ b/macros.xml Thu Dec 05 07:39:41 2019 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.12.0</token> - <token name="@GALAXY_TOOL_VERSION@">0</token> + <token name="@GALAXY_TOOL_VERSION@">1</token> <xml name="requirements"> <requirements>
--- a/purityA.R Wed Nov 27 14:20:07 2019 -0500 +++ b/purityA.R Thu Dec 05 07:39:41 2019 -0500 @@ -6,9 +6,9 @@ make_option(c("-o", "--out_dir"), type="character"), make_option("--mzML_files", type="character"), make_option("--galaxy_names", type="character"), - make_option("--minOffset", default=0.5), - make_option("--maxOffset", default=0.5), - make_option("--ilim", default=0.05), + make_option("--minOffset", type="numeric"), + make_option("--maxOffset", type="numeric"), + make_option("--ilim", type="numeric"), make_option("--iwNorm", default="none", type="character"), make_option("--exclude_isotopes", action="store_true"), make_option("--isotope_matrix", type="character"), @@ -22,18 +22,26 @@ opt <- parse_args(OptionParser(option_list=option_list)) print(opt) -minOffset = as.numeric(opt$minOffset) -maxOffset = as.numeric(opt$maxOffset) if (opt$iwNorm=='none'){ iwNorm = FALSE iwNormFun = NULL }else if (opt$iwNorm=='gauss'){ iwNorm = TRUE - iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) + if (is.null(opt$minOffset) || is.null(opt$maxOffset)){ + print('User has to define offsets if using Gaussian normalisation') + }else{ + iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset), + maxOff=as.numeric(opt$maxOffset)) + } }else if (opt$iwNorm=='rcosine'){ iwNorm = TRUE - iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) + if (is.null(opt$minOffset) || is.null(opt$maxOffset)){ + print('User has to define offsets if using R-cosine normalisation') + }else{ + iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset), + maxOff=as.numeric(opt$maxOffset)) + } }else if (opt$iwNorm=='QE5'){ iwNorm = TRUE iwNormFun = msPurity::iwNormQE.5()