| Previous changeset 14:45b4ede6940e (2020-01-24) |
|
Commit message:
"planemo upload commit 6bc2c32177acd823d5025bc90a562e6e6b2a233a" |
|
modified:
goprofiles.R goprofiles.xml |
| b |
| diff -r 45b4ede6940e -r 601027649251 goprofiles.R --- a/goprofiles.R Fri Jan 24 05:10:14 2020 -0500 +++ b/goprofiles.R Tue Apr 06 16:59:30 2021 +0000 |
| [ |
| b'@@ -1,12 +1,14 @@\n-options(warn=-1) #TURN OFF WARNINGS !!!!!!\n+options(warn = -1) #TURN OFF WARNINGS !!!!!!\n \n # Load necessary libraries\n-suppressMessages(library(goProfiles,quietly = TRUE))\n+suppressMessages(library(goProfiles, quietly = TRUE))\n \n # Read file and return file content as data.frame\n-read_file <- function(path,header){\n- file <- try(read.csv(path,header=header, sep="\\t",stringsAsFactors = FALSE, quote="\\"", check.names = F),silent=TRUE)\n- if (inherits(file,"try-error")){\n+read_file <- function(path, header) {\n+ file <- try(read.csv(path, header = header,\n+ sep = "\\t", stringsAsFactors = FALSE,\n+ quote = "\\"", check.names = F), silent = TRUE)\n+ if (inherits(file, "try-error")) {\n stop("File not found !")\n }else{\n return(file)\n@@ -14,27 +16,30 @@\n }\n \n #convert a string to boolean\n-str2bool <- function(x){\n- if (any(is.element(c("t","true"),tolower(x)))){\n- return (TRUE)\n- }else if (any(is.element(c("f","false"),tolower(x)))){\n- return (FALSE)\n+str2bool <- function(x) {\n+ if (any(is.element(c("t", "true"), tolower(x)))) {\n+ return(TRUE)\n+ }else if (any(is.element(c("f", "false"), tolower(x)))) {\n+ return(FALSE)\n }else{\n return(NULL)\n }\n }\n \n-check_ids <- function(vector,type) {\n- uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"\n- entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"\n- if (type == "Entrez"){\n- return(grepl(entrez_id,vector))\n+check_ids <- function(vector, type) {\n+ # nolint start\n+ uniprot_pattern <-\n+ "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"\n+ entrez_id <- "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"\n+ # nolint end\n+ if (type == "Entrez") {\n+ return(grepl(entrez_id, vector))\n } else if (type == "UniProt") {\n- return(grepl(uniprot_pattern,vector))\n+ return(grepl(uniprot_pattern, vector))\n }\n }\n \n-getprofile = function(ids, id_type, level, duplicate,species) {\n+getprofile <- function(ids, id_type, level, duplicate, species) {\n ####################################################################\n # Arguments\n # - ids: list of input IDs\n@@ -43,89 +48,100 @@\n # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)\n # - species\n ####################################################################\n- \n+\n library(species, character.only = TRUE, quietly = TRUE)\n- \n- if (species=="org.Hs.eg.db"){\n- package=org.Hs.eg.db\n- } else if (species=="org.Mm.eg.db"){\n- package=org.Mm.eg.db\n- } else if (species=="org.Rn.eg.db"){\n- package=org.Rn.eg.db\n+\n+ if (species == "org.Hs.eg.db") {\n+ package <- org.Hs.eg.db #nolint\n+ } else if (species == "org.Mm.eg.db") {\n+ package <- org.Mm.eg.db #nolint\n+ } else if (species == "org.Rn.eg.db") {\n+ package <- org.Rn.eg.db #nolint\n }\n- \n+\n # Check if level is number\n if (! as.numeric(level) %% 1 == 0) {\n stop("Please enter an integer for level")\n } else {\n- level = as.numeric(level)\n+ level <- as.numeric(level)\n }\n- #genes = as.vector(file[,ncol])\n- \n+\n+\n # Extract Gene Entrez ID\n if (id_type == "Entrez") {\n- id = select(package, ids, "ENTREZID", multiVals = "first")\n+ id <- select(package, ids, "ENTREZID", multiVals = "first") #nolint\n } else {\n- id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")\n+ id <- select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first") #nolint\n+ }\n+ if (duplicate) {\n+ id <- unique(id)\n }\n- if (duplicate) { id = unique(id) }\n- genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]\n- NAs = id$UNIPROT[which(is.na(id$ENTREZID))] # IDs that have NA ENTREZID\n- \n+ genes_ids <- id$ENTREZID[which(!is.na(id$ENTREZID))]\n+ nas <- id$UNIPROT[which(is.na(id$ENTREZID))] # IDs that have NA ENTREZID #nolint\n+\n # Create basic profiles\n- profile.CC = basicProfile(genes_ids, onto=\'CC\', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)'..b' --text_output: text output filename \\n\n --species")\n- q(save="no")\n+ q(save = "no")\n }\n- \n+\n # Parse arguments\n- parseArgs <- function(x) strsplit(sub("^--", "", x), "=")\n- argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))\n- args <- as.list(as.character(argsDF$V2))\n- names(args) <- argsDF$V1\n+ parse_args <- function(x) strsplit(sub("^--", "", x), "=")\n+ args_df <- as.data.frame(do.call("rbind", parse_args(args)))\n+ args <- as.list(as.character(args_df$V2))\n+ names(args) <- args_df$V1\n \n- #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")\n- #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")\n- \n- id_type = args$id_type\n- input_type = args$input_type\n+\n+ id_type <- args$id_type\n+ input_type <- args$input_type\n if (input_type == "text") {\n- input = unlist(strsplit(strsplit(args$input, "[ \\t\\n]+")[[1]],";"))\n+ input <- unlist(strsplit(strsplit(args$input, "[ \\t\\n]+")[[1]], ";"))\n } else if (input_type == "file") {\n- filename = args$input\n- ncol = args$ncol\n+ filename <- args$input\n+ ncol <- args$ncol\n # Check ncol\n if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {\n stop("Please enter an integer for level")\n } else {\n- ncol = as.numeric(gsub("c", "", ncol))\n+ ncol <- as.numeric(gsub("c", "", ncol))\n }\n- header = str2bool(args$header)\n+ header <- str2bool(args$header)\n # Get file content\n- file = read_file(filename, header)\n+ file <- read_file(filename, header)\n # Extract Protein IDs list\n- input = unlist(strsplit(as.character(file[,ncol]),";"))\n+ input <- unlist(strsplit(as.character(file[, ncol]), ";"))\n }\n- input = input [which(!is.na(gsub("NA",NA,input)))]\n- \n- if (! any(check_ids(input,id_type))){\n- stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))\n+ input <- input [which(!is.na(gsub("NA", NA, input)))]\n+\n+ if (! any(check_ids(input, id_type))) {\n+ stop(paste(id_type,\n+ "not found in your ids list, please check your IDs in input\n+ or the selected column of your input file"))\n }\n- \n- ontoopt = strsplit(args$onto_opt, ",")[[1]]\n- onto_pos = as.integer(gsub("BP",3,gsub("MF",2,gsub("CC",1,ontoopt))))\n- plotopt = args$plot_opt\n- level = args$level\n- per = as.logical(args$per)\n- title = args$title\n- duplicate = str2bool(args$duplicate)\n- text_output = args$text_output\n- species=args$species\n+\n+ ontoopt <- strsplit(args$onto_opt, ",")[[1]]\n+ onto_pos <- as.integer(gsub("BP", 3, gsub("MF", 2, gsub("CC", 1, ontoopt))))\n+ plotopt <- args$plot_opt\n+ level <- args$level\n+ per <- as.logical(args$per)\n+ title <- args$title\n+ duplicate <- str2bool(args$duplicate)\n+ text_output <- args$text_output\n+ species <- args$species\n \n- profiles = getprofile(input, id_type, level, duplicate,species)\n- \n+ profiles <- getprofile(input, id_type, level, duplicate, species)\n+\n for (index in onto_pos) {\n- onto = names(profiles[index])\n- profile=profiles[index]\n- make_plot(profile,per,title,onto,plotopt)\n- text_output=paste("goProfiles_",onto,"_",title,".tsv",sep="",collapse="")\n- profile = as.data.frame(profile)\n- profile <- as.data.frame(apply(profile, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" and " " to NA\n- write.table(profile, text_output, sep="\\t", row.names = FALSE, quote=FALSE, col.names = T)\n+ onto <- names(profiles[index])\n+ profile <- profiles[index]\n+ make_plot(profile, per, title, onto, plotopt)\n+ text_output <- paste("goProfiles_", onto, "_",\n+ title, ".tsv", sep = "", collapse = "")\n+ profile <- as.data.frame(profile)\n+ profile <- as.data.frame(apply(profile, c(1, 2),\n+ function(x) gsub("^$|^ $", NA, x))) #convert "" and " " to NA\n+ write.table(profile, text_output, sep = "\\t",\n+ row.names = FALSE, quote = FALSE, col.names = T)\n }\n }\n \n' |
| b |
| diff -r 45b4ede6940e -r 601027649251 goprofiles.xml --- a/goprofiles.xml Fri Jan 24 05:10:14 2020 -0500 +++ b/goprofiles.xml Tue Apr 06 16:59:30 2021 +0000 |
| [ |
| @@ -1,14 +1,13 @@ -<tool id="goProfiles" name="Compute functional profiles" version="2020.01.23"> +<tool id="goProfiles" name="Compute functional profiles" version="2021.04.03"> <description>(Human, Mouse) [goProfiles]</description> <requirements> - <requirement type="package" >R</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> - <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement--> - <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement> - <requirement type="package" version="2.44.0">bioconductor-biobase</requirement> - <requirement type="package" version="1.46.0">bioconductor-goprofiles</requirement> - + <requirement type="package" version="4.0.3">r-base</requirement> + <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement> + <requirement type="package" version="2.50.0">bioconductor-biobase</requirement> + <requirement type="package" version="3.12.1">bioconductor-go.db</requirement> + <requirement type="package" version="1.52.0">bioconductor-goprofiles</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -135,9 +134,9 @@ <param name="title" value="Test" /> <param name="plot_opt" value="PDF" /> <output_collection name="output" type="list" > - <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/> - <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/> - <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/> + <element name="profile_BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/> + <element name="profile_CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/> + <element name="profile_MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/> </output_collection> <output name="log" file="GO_Profile_text_output.tsv"/> </test> @@ -183,11 +182,12 @@ .. class:: infomark Packages used: - - bioconductor-org.hs.eg.db v3.5.0 - - bioconductor-org.mm.eg.db v3.5.0 - - bioconductor-annotationdbi v1.40.0 - - bioconductor-biobase v2.98.0 - - goprofiles v1.38.0 + - bioconductor-org.hs.eg.db v3.12.0 + - bioconductor-org.mm.eg.db v3.12.0 + - bioconductor-annotationdbi v1.52.0 + - bioconductor-biobase v2.50.0 + - bioconductor-go.db v3.12.1 + - goprofiles v1.52.0 ----- |