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Commit message:
planemo upload commit eb7450f36863f02f036cbc52bf5525d68f22bd9e |
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modified:
README.rst add_expression_HPA.R |
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add_expression_data.xml |
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removed:
expression_rnaseq_abbased.xml |
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| diff -r 2df5166efebb -r 5c260bd3552e README.rst --- a/README.rst Fri Mar 23 10:31:59 2018 -0400 +++ b/README.rst Tue Dec 18 08:23:48 2018 -0500 |
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| @@ -2,7 +2,7 @@ ========================================================= **Authors** -Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform @@ -20,7 +20,7 @@ **Databases** -HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz +HPA source file: http://www.proteinatlas.org/download/proteinatlas.tab.gz **Annotation** @@ -46,4 +46,4 @@ **Outputs** -The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. +The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. |
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| diff -r 2df5166efebb -r 5c260bd3552e add_expression_HPA.R --- a/add_expression_HPA.R Fri Mar 23 10:31:59 2018 -0400 +++ b/add_expression_HPA.R Tue Dec 18 08:23:48 2018 -0500 |
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| @@ -1,40 +1,94 @@ # Read file and return file content as data.frame -readfile = function(filename, header) { - if (header == "true") { - # Read only first line of the file as header: - headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "") - #Read the data of the files (skipping the first row) - file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "") - # Remove empty rows - file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] - #And assign the header to the data - names(file) <- headers +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) } - else { - file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "") - # Remove empty rows - file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] +} + +#convert a string to boolean +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) } - return(file) } add_expression = function(input, atlas, options) { + input <- unique(input[!is.na(input)]) + input <- gsub("[[:blank:]]|\u00A0","",input) if (all(!input %in% atlas$Ensembl)) { return(NULL) - } - else { - res = matrix(nrow=length(input), ncol=0) - names = c() - for (opt in options) { - names = c(names, opt) - info = atlas[match(input, atlas$Ensembl,incomparable="NA"),][opt][,] - res = cbind(res, info) - } - colnames(res) = names + } else { + res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)] + res = res[which(!is.na(res[,1])),] + row.names(res)=res[,1] + res=res[2:ncol(res)] + res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA return(res) } } +order_columns <- function (df,ncol){ + if (ncol==1){ #already at the right position + return (df) + } else { + df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])] + } + return (df) +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + main = function() { args <- commandArgs(TRUE) if(length(args)<1) { @@ -63,59 +117,52 @@ args <- as.list(as.character(argsDF$V2)) names(args) <- argsDF$V1 + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda") + inputtype = args$inputtype if (inputtype == "copypaste") { input = strsplit(args$input, "[ \t\n]+")[[1]] - } - else if (inputtype == "tabfile") { + } else if (inputtype == "tabfile") { filename = args$input ncol = args$column # Check ncol if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) { stop("Please enter an integer for level") - } - else { + } else { ncol = as.numeric(gsub("c", "", ncol)) } - header = args$header - # Get file content - file = readfile(filename, header) - # Extract Protein IDs list - input = c() - for (row in as.character(file[,ncol])) { - input = c(input, strsplit(row, ";")[[1]][1]) - } + header = str2bool(args$header) + file = read_file(filename, header) + file = one_id_one_line(file,ncol) + input = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)) + input = input[which(!is.na(input))] } # Read protein atlas protein_atlas = args$atlas - protein_atlas = readfile(protein_atlas, "true") + protein_atlas = read_file(protein_atlas, T) # Add expression output = args$output - names = c() options = strsplit(args$select, ",")[[1]] res = add_expression(input, protein_atlas, options) - + # Write output if (is.null(res)) { write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE) - } - else { + } else { if (inputtype == "copypaste") { - names = c("Ensembl", colnames(res)) - res = cbind(as.matrix(input), res) - colnames(res) = names - write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE) + input <- data.frame(input) + output_content = merge(input,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T) + colnames(output_content)[1] = "Ensembl" + } else if (inputtype == "tabfile") { + output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T) + output_content = order_columns(output_content,ncol) } - else if (inputtype == "tabfile") { - names = c(names(file), colnames(res)) - output_content = cbind(file, res) - colnames(output_content) = names - write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) - } + output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) + write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) } - } main() |
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| diff -r 2df5166efebb -r 5c260bd3552e add_expression_data.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_expression_data.xml Tue Dec 18 08:23:48 2018 -0500 |
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| @@ -0,0 +1,157 @@ +<tool id="rna_abbased_data" name="Add expression data" version="2018.12.12"> +<description> (RNAseq or Immuno-assays)[Human Protein Atlas] +</description> +<requirements> + <requirement type="package" version="3.4.1">R</requirement> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> +<command><![CDATA[ + + #if $inputtype.filetype == "copy_paste": + + Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' + + #else + + Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output' + + #end if + + +]]></command> + +<inputs> + <conditional name="inputtype"> + <param name="filetype" type="select" label="Enter your IDs (Ensembl gene ENSG IDs only)" help="Copy/paste or from a file (e.g. table)"> + <option value="file_all" selected="true">Input file containing your IDs</option> + <option value="copy_paste">Copy/paste your list of IDs</option> + </param> + <when value="copy_paste"> + <param name="genelist" type="text" label="Enter a list of IDs"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file_all"> + <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> + <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/> + <param name="header" type="select" label="Does file contain header?" multiple="false" optional="false"> + <option value="true" selected="true">Yes</option> + <option value="false" selected="false">No</option> + </param> + </when> + </conditional> + <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> + <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > + <option value="Gene" selected="true">Gene name</option> + <option value="Gene description" selected="false">Gene description</option> + <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> + <option value="Antibody">Antibody reference</option> + <option value="RNA tissue category">RNA tissue category</option> + <option value="Reliability (IH)">IH detection level</option> + <option value="Reliability (IF)">IF detection level</option> + <option value="Subcellular location">Subcellular location</option> + <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> + <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> + </param> + </section> + +</inputs> + + +<outputs> + <data name="output" format="tsv" label=""/> +</outputs> + +<tests> + <test> + <conditional name="inputtype"> + <param name="filetype " value="file_all"/> + <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> + <param name="column" value="c8"/> + <param name="header" value="TRUE"/> + </conditional> + <section name="options"> + <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/> + </section> + <output name="output" file="Get_annotation_RNAseq.txt"/> + </test> +</tests> + +<help><![CDATA[ +**Description** + +This tool adds expression annotation (RNAseq- or antibody-based experimental data - see "Parameters" below) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your gene/protein list. + +----- + +**Input** + +Input can be either a list of Ensembl gene (ENSG) IDsds (copy/paste mode) or a file containing multiple fields with at least one column of Ensembl gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. + +----- + +**Parameters** + +"Select information to add to your list": choose by clicking the following information: + +- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) + +- Gene description: entry description (full text) + +- Evidence: at protein level, at transcript level or no evidence + +- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF + +- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . + +- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . + +- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . + +- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa + +- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. + +- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. + +----- + +**Output** + +The output is a tabular file containing original columns and new columns including selected annotation. + +----- + +**Data sources (release date)** + +HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz + +----- + +.. class:: infomark + +**Authors** + +Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, 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> +</citations> + +</tool> |
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| diff -r 2df5166efebb -r 5c260bd3552e expression_rnaseq_abbased.xml --- a/expression_rnaseq_abbased.xml Fri Mar 23 10:31:59 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,147 +0,0 @@ -<tool id="rna_abbased_data" name="Add expression data to your protein list" version="0.1.0"> -<description> -mRNA and protein level data from Human Protein Atlas -</description> -<requirements> - <requirement type="package" version="3.4.1">R</requirement> -</requirements> -<stdio> - <exit_code range="1:" /> -</stdio> -<command><![CDATA[ - - #if $inputtype.filetype == "copy_paste": - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' - - #else - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output' - - #end if - - -]]></command> - -<inputs> - <conditional name="inputtype"> - <param name="filetype" type="select" label="Enter your list of Ensembl gene ID"> - <option value="file_all" selected="true">Input file containing your IDs</option> - <option value="copy_paste">Copy/paste your list of IDs</option> - </param> - <when value="copy_paste"> - <param name="genelist" type="text" label="Enter a list of identifiers"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - <when value="file_all"> - <param name="genelist" type="data" format="txt,tabular" label="Choose your file" help="This file must imperatively have 1 column filled with Ensembl Gene IDs (ENSG). Please use the ID_Converter tool if this is not the case."/> - <param name="column" type="text" label="Please specify the column where are your Ensembl gene IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/> - <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> - <option value="true" selected="true">Yes</option> - <option value="false" selected="false">No</option> - </param> - </when> - </conditional> - <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> - <param name="hpaparams" type="select" label="Choose the information from RNAseq/ab-based data you want to add to your list (see below for details)" multiple="True" display="checkboxes"> - <option value="Gene" selected="true">Gene name</option> - <option value="Gene description" selected="false">Gene description</option> - <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> - <option value="Antibody">Antibody reference</option> - <option value="RNA tissue category">RNA tissue category</option> - <option value="Reliability (IH)">IH detection level</option> - <option value="Reliability (IF)">IF detection level</option> - <option value="Subcellular location">Subcellular location</option> - <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> - <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> - </param> - </section> - -</inputs> - - -<outputs> - <data name="output" format="tabular" label=""/> -</outputs> - -<tests> - <test> - <conditional name="inputtype"> - <param name="filetype " value="file_all"/> - <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> - <param name="column" value="c8"/> - <param name="header" value="TRUE"/> - </conditional> - <section name="options"> - <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/> - </section> - <output name="output" file="Get_annotation_RNAseq.txt"/> - </test> -</tests> - -<help><![CDATA[ - -This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list. - -**Input** - -Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. - -**Databases** - -HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz - -**Annotation** - -- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) - -- Gene description: entry description (full text) - -- Evidence: at protein level, at transcript level or no evidence - -- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF - -- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . - -- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . - -- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . - -- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa - -- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. - -- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. - -**Outputs** - -The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. - ------ - -.. class:: infomark - -**Authors** - -Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR - -Sandra Dérozier, Olivier Rué, Christophe Caron, 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> -</citations> - -</tool> |