Mercurial > repos > proteore > proteore_kegg_pathways_coverage
changeset 3:e7b3609160c5 draft
planemo upload commit 6854718828a7478905b41fb92d6f96ab41896e84-dirty
| author | proteore |
|---|---|
| date | Tue, 14 May 2019 08:51:46 -0400 |
| parents | 179bfc3c7938 |
| children | dc39f12f96d1 |
| files | compute_kegg_pathways.R compute_kegg_pathways.xml kegg_identification.R kegg_identification.xml test-data/SPZ.soluble.txt |
| diffstat | 5 files changed, 363 insertions(+), 305 deletions(-) [+] |
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--- a/compute_kegg_pathways.R Thu Nov 22 04:38:42 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -options(warn=-1) #TURN OFF WARNINGS !!!!!! - -suppressMessages(library(KEGGREST)) - -get_args <- function(){ - - ## Collect arguments - args <- commandArgs(TRUE) - - ## Default setting when no arguments passed - if(length(args) < 1) { - args <- c("--help") - } - - ## Help section - if("--help" %in% args) { - cat("Pathview R script - Arguments: - --help Print this test - --input tab file - --id_list id list ',' separated - --id_type type of input ids (kegg-id, uniprot_AC,geneID) - --id_column number og column containg ids of interest - --nb_pathways number of pathways to return - --header boolean - --output output path - --species species used to get specific pathways (hsa,mmu,rno) - - Example: - Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE \n\n") - - q(save="no") - } - - parseArgs <- function(x) strsplit(sub("^--", "", x), "=") - argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) - args <- as.list(as.character(argsDF$V2)) - names(args) <- argsDF$V1 - - return(args) -} - -str2bool <- function(x){ - if (any(is.element(c("t","true"),tolower(x)))){ - return (TRUE) - }else if (any(is.element(c("f","false"),tolower(x)))){ - return (FALSE) - }else{ - return(NULL) - } -} - -read_file <- function(path,header){ - file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) - if (inherits(file,"try-error")){ - stop("File not found !") - }else{ - return(file) - } -} - -get_pathways_list <- function(species){ - ##all available pathways for the species - pathways <-keggLink("pathway", species) - tot_path<-unique(pathways) - - ##formating the dat into a list object - ##key= pathway ID, value = genes of the pathway in the kegg format - pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway))) - return (pathways_list) -} - -get_list_from_cp <-function(list){ - list = strsplit(list, "[ \t\n]+")[[1]] - list = list[list != ""] #remove empty entry - list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") - return(list) -} - -geneID_to_kegg <- function(vector,species){ - vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F) - return (vector) -} - -to_keggID <- function(id_list,id_type){ - if (id_type == "ncbi-geneid") { - id_list <- unique(geneID_to_kegg(id_list,args$species)) - } else if (id_type=="uniprot"){ - id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F)) - if (length(id_list)>250){ - id_list <- split(id_list, ceiling(seq_along(id_list)/250)) - id_list <- sapply(id_list, function(x) keggConv("genes",x)) - id_list <- unique(unlist(id_list)) - } else { - id_list <- unique(keggConv("genes", id_list)) - } - } else if (id_type=="kegg-id") { - id_list <- unique(id_list) - } - return (id_list) -} - -kegg_mapping<- function(kegg_id_list,id_type,ref_ids) { - - #mapping - map<-lapply(ref_ids, is.element, unique(kegg_id_list)) - names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:" - - in.path<-sapply(map, function(x) length(which(x==TRUE))) - tot.path<-sapply(map, length) - - ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)])) - ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2)) - - ##useful but LONG - ## to do before : in step 1 - path.names<-names(in.path[which(in.path!=0)]) - name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE) - - res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)])) - res <- res[order(as.numeric(res[,3]),decreasing = TRUE),] - colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway") - - return(res) - -} - -#get args from command line -args <- get_args() - -#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda") -#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda") - -###setting variables -header = str2bool(args$header) -if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)} #get ids from copy/paste input -if (!is.null(args$input)) { #get ids from input file - csv <- read_file(args$input,header) - ncol <- as.numeric(gsub("c", "" ,args$id_column)) - id_list <- as.vector(csv[,ncol]) - id_list <- id_list[which(!is.na(id_list))] -} - -#convert to keggID if needed -id_list <- to_keggID(id_list,args$id_type) - -#get pathways of species with associated KEGG ID genes -pathways_list <- get_pathways_list(args$species) - -#mapping on pathways -res <- kegg_mapping(id_list,args$id_type,pathways_list) -if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] } - -write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE) -
--- a/compute_kegg_pathways.xml Thu Nov 22 04:38:42 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -<tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.22"> - <description>identification and coverage</description> - <requirements> - <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - Rscript $__tool_directory__/compute_kegg_pathways.R - - #if $input.ids == "text" - --id_list="$input.txt" - #else - --input="$input.file" - --id_column="$input.ncol" - --header="$input.header" - #end if - - --id_type="$id_type" - --output="$output1" - --nb_pathways="$nb_pathways" - --species="$species" - - ]]></command> - <inputs> - <conditional name="input" > - <param name="ids" type="select" label="Enter your list of identifiers" help="Copy/paste or ID list from a file (e.g. table)" > - <option value="text">Copy/paste your identifiers</option> - <option value="file" selected="true">Input file containing your identifiers</option> - </param> - <when value="text" > - <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' > - <sanitizer invalid_char=''> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - <when value="file" > - <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of identifiers" help="" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain a header?" /> - <param name="ncol" type="text" value="c1" label="The column number of your identifiers to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> - </when> - </conditional> - <param name="id_type" type="select" label="select your identifiers type :" > - <option value="ncbi-geneid" selected="true">Entrez genes ID</option> - <option value="kegg-id">KEGG genes ID</option> - <option value="uniprot">Uniprot Accession number</option> - - </param> - <param name="species" type="select" label="Select species"> - <option value="hsa">Human (H. sapiens)</option> - <option value="mmu">Mouse (M. musculus)</option> - <option value="rno">Rat (R. norvegicus)</option> - </param> - <param type="integer" name="nb_pathways" label="Set the number of pathways to be displayed in the output" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/> - </inputs> - <outputs> - <data name="output1" format="tsv" /> - </outputs> - <tests> - <test> - <conditional name="input" > - <param name="ids" value="file"/> - <param name="file" value="SPZ.soluble_kegg_id.txt" /> - <param name="header" value="true" /> - <param name="ncol" value="c2" /> - </conditional> - <param name="id_type" value="kegg-id" /> - <param name="species" value="hsa" /> - <param name="nb_pathways" value="20" /> - <output name="output1" value="test.tsv" /> - </test> - </tests> - <help><![CDATA[ - -This tool maps a list of identifiers to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. - -It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset. - -By default the number of pathway to be displayed is set to 10 and sorted in descending order. - -At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus). - -**Input:** - -Input can be either a list of ids or a file containing multiple columns but with at least one column of ids (e.g. hsa04970). -Input ids type can be Entrez gene ID, KEGG gene ID or Uniprot accession number. - -.. class:: warningmark - -If you use Uniprot accession number, it will be converted to KEGG gene ID, this step can be time consuming. -If your input file contains other type of ids, please use the ID_Converter tool. - -**Output:** - -The output is a tabular file (.tsv) with the following columns: - -* **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970) -* **Description:** name of the pathway as in KEGG -* **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage -* **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes of your list mapped on the KEGG pathway -* **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway - ------ - -.. class:: infomark - -**Database:** - -Pathways and KEGG genes IDs are collected via KEGGREST package. - -User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html - - ------ - -.. class:: infomark - -**Galaxy integration** - -David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR - -Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform - -This work has been partially funded through the French National Agency for Research (ANR) IFB project. - -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. - - ]]></help> - <citations> - <citation type="bibtex"> -@misc{githubKEGGREST, - title = {KEGGREST: Client-side REST access to KEGG}, - author = {Dan Tenenbaum}, - year = {2018}, - note = {R package version 1.18.1}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/Bioconductor/KEGGREST}, -}</citation> - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_identification.R Tue May 14 08:51:46 2019 -0400 @@ -0,0 +1,204 @@ +options(warn=-1) #TURN OFF WARNINGS !!!!!! + +suppressMessages(library(KEGGREST)) + +get_args <- function(){ + + ## Collect arguments + args <- commandArgs(TRUE) + + ## Default setting when no arguments passed + if(length(args) < 1) { + args <- c("--help") + } + + ## Help section + if("--help" %in% args) { + cat("Pathview R script + Arguments: + --help Print this test + --input tab file + --id_list id list ',' separated + --id_type type of input ids (kegg-id, uniprot_AC,geneID) + --id_column number og column containg ids of interest + --nb_pathways number of pathways to return + --header boolean + --output output path + --species species used to get specific pathways (hsa,mmu,rno) + + Example: + Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE \n\n") + + q(save="no") + } + + parseArgs <- function(x) strsplit(sub("^--", "", x), "=") + argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) + args <- as.list(as.character(argsDF$V2)) + names(args) <- argsDF$V1 + + return(args) +} + +str2bool <- function(x){ + if (any(is.element(c("t","true"),tolower(x)))){ + return (TRUE) + }else if (any(is.element(c("f","false"),tolower(x)))){ + return (FALSE) + }else{ + return(NULL) + } +} + +read_file <- function(path,header){ + file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + return(file) + } +} + +get_pathways_list <- function(species){ + ##all available pathways for the species + pathways <-keggLink("pathway", species) + tot_path<-unique(pathways) + + ##formating the dat into a list object + ##key= pathway ID, value = genes of the pathway in the kegg format + pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway))) + return (pathways_list) +} + +get_list_from_cp <-function(list){ + list = gsub(";","\t",list) + list = strsplit(list, "[ \t\n]+")[[1]] + list = gsub("[[:blank:]]|\u00A0|NA","",list) + list = list[which(!is.na(list[list != ""]))] #remove empty entry + list = unique(gsub("-.+", "", list)) #Remove isoform accession number (e.g. "-2") + return(list) +} + +geneID_to_kegg <- function(vector,species){ + vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F) + return (vector) +} + +to_keggID <- function(id_list,id_type){ + if (id_type == "ncbi-geneid") { + id_list <- unique(geneID_to_kegg(id_list,args$species)) + } else if (id_type=="uniprot"){ + id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F)) + if (length(id_list)>250){ + id_list <- split(id_list, ceiling(seq_along(id_list)/250)) + id_list <- sapply(id_list, function(x) keggConv("genes",x)) + id_list <- unique(unlist(id_list)) + } else { + id_list <- unique(keggConv("genes", id_list)) + } + } else if (id_type=="kegg-id") { + id_list <- unique(id_list) + } + return (id_list) +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + +kegg_mapping<- function(kegg_id_list,id_type,ref_ids) { + + #mapping + map<-lapply(ref_ids, is.element, unique(kegg_id_list)) + names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:" + + in.path<-sapply(map, function(x) length(which(x==TRUE))) + tot.path<-sapply(map, length) + + ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)])) + ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2)) + + ##useful but LONG + ## to do before : in step 1 + path.names<-names(in.path[which(in.path!=0)]) + name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE) + + res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)])) + res <- res[order(as.numeric(res[,3]),decreasing = TRUE),] + colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway") + + return(res) + +} + +#get args from command line +args <- get_args() + +#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_identification/args.Rda") +#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_identification/args.Rda") + +###setting variables +header = str2bool(args$header) +if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)} #get ids from copy/paste input +if (!is.null(args$input)) { #get ids from input file + csv <- read_file(args$input,header) + ncol <- as.numeric(gsub("c", "" ,args$id_column)) + csv <- one_id_one_line(csv,ncol) + id_list <- as.vector(csv[,ncol]) + id_list <- unique(id_list[which(!is.na(id_list[id_list!=""]))]) +} + +#convert to keggID if needed +id_list <- to_keggID(id_list,args$id_type) + +#get pathways of species with associated KEGG ID genes +pathways_list <- get_pathways_list(args$species) + +#mapping on pathways +res <- kegg_mapping(id_list,args$id_type,pathways_list) +if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] } + +write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_identification.xml Tue May 14 08:51:46 2019 -0400 @@ -0,0 +1,157 @@ +<tool id="kegg_identification" name="Pathways identification" version="2019.05.14"> + <description>and coverage [KEGG]</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/kegg_identification.R + + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + + --id_type="$id_type" + --output="$output1" + --nb_pathways="$nb_pathways" + --species="$species" + + ]]></command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" > + <option value="text">Copy/paste your IDs</option> + <option value="file" selected="true">Input file containing your IDs</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular,tsv" label="Select your file" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> + </when> + </conditional> + <param name="id_type" type="select" label="Select IDs" > + <option value="ncbi-geneid" selected="true">Entrez Gene ID</option> + <option value="kegg-id">KEGG gene ID</option> + <option value="uniprot">UniProt Accession number</option> + + </param> + <param name="species" type="select" label="Species"> + <option value="hsa">Human (Homo sapiens)</option> + <option value="mmu">Mouse (Mus musculus)</option> + <option value="rno">Rat (Rattus norvegicus)</option> + </param> + <param type="integer" name="nb_pathways" label="Set number of pathways to be displayed" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/> + </inputs> + <outputs> + <data name="output1" format="tsv" /> + </outputs> + <tests> + <test> + <conditional name="input" > + <param name="ids" value="file"/> + <param name="file" value="SPZ.soluble_kegg_id.txt" /> + <param name="header" value="true" /> + <param name="ncol" value="c2" /> + </conditional> + <param name="id_type" value="kegg-id" /> + <param name="species" value="hsa" /> + <param name="nb_pathways" value="20" /> + <output name="output1" value="test.tsv" /> + </test> + </tests> + <help><![CDATA[ + +**Description** + +This tool maps a list of identifiers to all KEGG pathways and returns a list of KEGG pathways sorted by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes ID of the selected species for each KEGG pathway. + +It allows you to directly identify KEGG pathways that are the most covered by your gene/protein list. + +----- + +**Input** + +Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970). +Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671). + +.. class:: warningmark + +If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming. + +If your input file contains other type of ID, please use the ID_Converter tool. + +----- + +**Parameters** + +"Set number of pathways to be displayed": by default the number of pathway to be displayed is set to 10 and sorted in descending order. + +"Species": three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus). + +----- + +**Output:** + +The output is a tabular file (.tsv) with the following columns: + +* **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970) +* **Description:** name of the pathway as in KEGG +* **Ratio IDs mapped/total IDs (%):** pathway coverage in percentage +* **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes from your list mapped to the KEGG pathway +* **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway + +----- + +.. class:: infomark + +**Data source (release date)** + +Pathways and KEGG genes IDs are collected via KEGGREST package. + +User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html + +----- + +.. class:: infomark + +**Galaxy integration** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubKEGGREST, + title = {KEGGREST: Client-side REST access to KEGG}, + author = {Dan Tenenbaum}, + year = {2018}, + note = {R package version 1.18.1}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/Bioconductor/KEGGREST}, +}</citation> + </citations> +</tool>
--- a/test-data/SPZ.soluble.txt Thu Nov 22 04:38:42 2018 -0500 +++ b/test-data/SPZ.soluble.txt Tue May 14 08:51:46 2019 -0400 @@ -118,16 +118,13 @@ Q8WXX0 P13639 Q14697 -P55809 -A0AVT1 +P55809;A0AVT1 O14980 Q9BVA1 Q14697 O95202 O75694 -Q16851 -P26640 -P23368 +Q16851;P26640;P23368 P55084 P17174 P07814