Mercurial > repos > computational-metabolomics > mspurity_purityx
diff createMSP.R @ 6:6b9a83e08467 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
---|---|
date | Thu, 04 Mar 2021 12:25:25 +0000 |
parents | 1cba235b1972 |
children | b16952cc06d2 |
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--- a/createMSP.R Fri Nov 13 09:47:47 2020 +0000 +++ b/createMSP.R Thu Mar 04 12:25:25 2021 +0000 @@ -4,39 +4,40 @@ # Get the parameter option_list <- list( - make_option("--rdata_input",type="character"), - make_option("--method",type="character"), - make_option("--metadata",type="character"), - make_option("--metadata_cols",type="character"), - make_option("--metadata_cols_filter",type="character"), - make_option("--adduct_split", action="store_true"), - make_option("--xcms_groupids",type="character"), - make_option("--filter",action="store_true"), - make_option("--intensity_ra",type="character"), - make_option("--include_adducts",type="character"), - make_option("--msp_schema",type="character"), - make_option("--include_adducts_custom",type="character", default=""), - make_option("--out_dir",type="character", default=".") + make_option("--rdata_input", type = "character"), + make_option("--method", type = "character"), + make_option("--metadata", type = "character"), + make_option("--metadata_cols", type = "character"), + make_option("--metadata_cols_filter", type = "character"), + make_option("--adduct_split", action = "store_true"), + make_option("--xcms_groupids", type = "character"), + make_option("--filter", action = "store_true"), + make_option("--intensity_ra", type = "character"), + make_option("--include_adducts", type = "character"), + make_option("--msp_schema", type = "character"), + make_option("--include_adducts_custom", type = "character", default = ""), + make_option("--out_dir", type = "character", default = ".") ) -opt <- parse_args(OptionParser(option_list=option_list)) +opt <- parse_args(OptionParser(option_list = option_list)) print(opt) load(opt$rdata_input) -if (is.null(opt$metadata)){ +if (is.null(opt$metadata)) { metadata <- NULL }else{ - metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE) + metadata <- read.table(opt$metadata, header = TRUE, sep = "\t", + stringsAsFactors = FALSE, check.names = FALSE) - if(!opt$metadata_cols_filter==''){ - metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]] + if (!opt$metadata_cols_filter == "") { + metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]] - metadata <- metadata[,metadata_cols_filter, drop=FALSE] + metadata <- metadata[, metadata_cols_filter, drop = FALSE] print(metadata) - if (!"grpid" %in% colnames(metadata)){ - metadata$grpid <- 1:nrow(metadata) + if (!"grpid" %in% colnames(metadata)) { + metadata$grpid <- seq_len(nrow(metadata)) } print(metadata) @@ -47,7 +48,7 @@ -if (is.null(opt$metadata_cols) || opt$metadata_cols==''){ +if (is.null(opt$metadata_cols) || opt$metadata_cols == "") { metadata_cols <- NULL }else{ metadata_cols <- opt$metadata_cols @@ -55,36 +56,33 @@ } -if(is.null(opt$adduct_split)){ +if (is.null(opt$adduct_split)) { adduct_split <- FALSE }else{ adduct_split <- TRUE } -if (is.null(opt$xcms_groupids)){ +if (is.null(opt$xcms_groupids)) { xcms_groupids <- NULL }else{ - xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]]) + xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]]) } - - - -if (is.null(opt$include_adducts_custom)){ - include_adducts_custom <- '' +if (is.null(opt$include_adducts_custom)) { + include_adducts_custom <- "" }else{ include_adducts_custom <- opt$include_adducts_custom } -if (opt$include_adducts=='None'){ - include_adducts <- '' +if (opt$include_adducts == "None") { + include_adducts <- "" }else{ include_adducts <- opt$include_adducts } -include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="") +include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "") include_adducts_all <- gsub("^,", "", include_adducts_all) include_adducts_all <- gsub(",$", "", include_adducts_all) @@ -96,7 +94,7 @@ -if(is.null(opt$filter)){ +if (is.null(opt$filter)) { filter <- FALSE }else{ filter <- TRUE @@ -105,15 +103,15 @@ msPurity::createMSP(pa, - msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'), + msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"), metadata = metadata, metadata_cols = metadata_cols, method = opt$method, adduct_split = adduct_split, xcms_groupids = xcms_groupids, filter = filter, - intensity_ra=opt$intensity_ra, - include_adducts=include_adducts_all, - msp_schema=opt$msp_schema) + intensity_ra = opt$intensity_ra, + include_adducts = include_adducts_all, + msp_schema = opt$msp_schema) -print('msp created') +print("msp created")