| Previous changeset 6:1a642de6db01 (2020-03-04) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070" |
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modified:
gtf2featureAnnotation.xml |
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removed:
gtf2featureAnnotation.R |
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| diff -r 1a642de6db01 -r 14b3f2a4523b gtf2featureAnnotation.R --- a/gtf2featureAnnotation.R Wed Mar 04 06:44:32 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,196 +0,0 @@ -#!/usr/bin/env Rscript - -# This script parses the GTF file to create a feature-wise annotation file with -# mitochondrial features flagged, to assist in annotation and QC of single-cell -# expression data analysis. - -suppressPackageStartupMessages(require(rtracklayer)) -suppressPackageStartupMessages(require(optparse)) - -ucfirst <- function (str) { - paste(toupper(substring(str, 1, 1)), tolower(substring(str, 2)), sep = "") -} - -die <- function(message){ - write(message, stderr()) - q(status = 1) -} - -cleanlist <- function(str){ - tolower(unlist(strsplit(str, ','))) -} - -cl <- commandArgs(trailingOnly = TRUE) - -option_list = list( - make_option( - c("-g", "--gtf-file"), - action = "store", - default = NA, - type = 'character', - help = "Path to a valid GTF file" - ), - make_option( - c("-t", "--feature-type"), - action = "store", - default = 'gene', - type = 'character', - help = 'Feature type to use (default: gene)' - ), - make_option( - c("-f", "--first-field"), - action = "store", - default = 'gene_id', - type = 'character', - help = 'Field to place first in output table (default: gene_id)' - ), - make_option( - c("-r", "--no-header"), - action = "store_false", - default = TRUE, - type = 'logical', - help = 'Suppress header on output' - ), - make_option( - c("-l", "--fields"), - action = "store", - default = NULL, - type = 'character', - help = 'Comma-separated list of output fields to retain (default: all)' - ), - make_option( - c("-m", "--mito"), - action = "store_true", - default = FALSE, - type = 'character', - help = 'Mark mitochondrial elements with reference to chromsomes and biotypes' - ), - make_option( - c("-n", "--mito-chr"), - action = "store", - default = 'mt,mitochondrion_genome,mito,m,chrM,chrMt', - type = 'character', - help = 'If specified, marks in a column called "mito" features on the specified chromosomes (case insensitive)' - ), - make_option( - c("-p", "--mito-biotypes"), - action = "store", - default = 'mt_trna,mt_rrna,mt_trna_pseudogene', - type = 'character', - help = 'If specified, marks in a column called "mito" features with the specified biotypes (case insensitve)' - ), - make_option( - c("-c", "--filter-cdnas"), - action = "store", - default = NULL, - type = 'character', - help = 'If specified, sequences in the provided FASTA-format cDNAs file will be filtered to remove entries not present in the annotation' - ), - make_option( - c("-d", "--filter-cdnas-field"), - action = "store", - default = 'transcript_id', - type = 'character', - help = 'Where --filter-cdnas is specified, what field should be used to compare to identfiers from the FASTA?' - ), - make_option( - c("-e", "--filter-cdnas-output"), - action = "store", - default = 'filtered.fa.gz', - type = 'character', - help = 'Where --filter-cdnas is specified, what file should the filtered sequences be output to?' - ), - make_option( - c("-u", "--version-transcripts"), - action = "store_true", - default = FALSE, - type = 'logical', - help = 'Where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes.' - ), - make_option( - c("-o", "--output-file"), - action = "store", - default = NA, - type = 'character', - help = 'Output file path' - ) -) - -opt <- parse_args(OptionParser(option_list = option_list), convert_hyphens_to_underscores = TRUE) - -if (is.na(opt$gtf_file)){ - die('ERROR: No input GTF file specified') -} - -if (is.na(opt$output_file)){ - die('ERROR: No output file specified') -} - -# Import the GTF - -print(paste('Reading', opt$gtf_file, 'elements of type', opt$feature_type)) -gtf <- import(opt$gtf_file, feature.type = opt$feature_type ) - -# Combine basic info (chromosomes, coordinates) with annotation found in GTF attributes - -anno <- cbind(chromosome = seqnames(gtf), as.data.frame(ranges(gtf)), elementMetadata(gtf)) -print(paste('Found', nrow(anno), 'features')) - -# Mark mitochondrial features - -if (opt$mito){ - anno$mito <- ucfirst(as.character(tolower(anno$gene_biotype) %in% cleanlist(opt$mito_biotypes) | tolower(anno$chromosome) %in% cleanlist(opt$mito_chr))) -} - -# If specified, put the desired field first - -if (! is.na(opt$first_field)){ - if (! opt$first_field %in% colnames(anno)){ - die(paste(first_field, 'is not a valid field')) - } - anno <- anno[,c(opt$first_field, colnames(anno)[colnames(anno) != opt$first_field])] -} - -# Version transcripts - -if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){ - has_transcript_version <- ! is.na(anno$transcript_version) - anno$transcript_id[has_transcript_version] <- paste(anno$transcript_id[has_transcript_version], anno$transcript_version[has_transcript_version], sep='.') -} - -# If specified, filter down a provided cDNA FASTA file - -if (! is.null(opt$filter_cdnas)){ - - print(paste("Filtering", opt$filter_cdnas, "to match the GTF")) - - suppressPackageStartupMessages(require(Biostrings)) - - cdna <- readDNAStringSet(opt$filter_cdnas) - cdna_transcript_names <- unlist(lapply(names(cdna), function(x) unlist(strsplit(x, ' '))[1] )) - - # Filter out cDNAs without matching transcript entries in the GTF - - if (! any(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])){ - die(paste("ERROR: None of the input sequences have matching", opt$filter_cdnas_field, 'values in the GTF file')) - } - - cdna <- cdna[which(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])] - - print(paste('Storing filtered seqeunces to', opt$filter_cdnas_output)) - writeXStringSet(x = cdna, filepath = opt$filter_cdnas_output, compress = 'gzip') -} - -# If specified, subset to desired fields - -if (! is.null(opt$fields) && opt$fields != ''){ - fields <- unlist(strsplit(opt$fields, ',')) - if (any(! fields %in% colnames(anno))){ - die(paste('ERROR:', fields, 'contains invalid field(s)')) - } - anno <- anno[,fields, drop = FALSE] - anno <- anno[apply(anno, 1, function(x) all(! is.na(x))), ] -} - -print(paste('Storing output to', opt$output_file)) -write.table(anno, file = opt$output_file, sep = "\t", quote=FALSE, row.names = FALSE, col.names = opt$no_header) |
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| diff -r 1a642de6db01 -r 14b3f2a4523b gtf2featureAnnotation.xml --- a/gtf2featureAnnotation.xml Wed Mar 04 06:44:32 2020 -0500 +++ b/gtf2featureAnnotation.xml Mon Jul 19 08:00:24 2021 +0000 |
| [ |
| @@ -1,13 +1,11 @@ -<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy6" profile="18.01"> +<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.52.0+galaxy0" profile="18.01"> <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description> <requirements> - <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> - <requirement type="package" version="2.50.2">bioconductor-biostrings</requirement> - <requirement type="package" version="1.6.4">r-optparse</requirement> + <requirement type="package" version="1.0.1">atlas-gene-annotation-manipulation</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -s '$gtf_input' input.gtf; - $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf + gtf2featureAnnotation.R --gtf-file input.gtf #if $noheader --no-header #end if @@ -17,8 +15,17 @@ #if $mito.mark_mito --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" #end if +#if $cdnas.parse_cdnas +--parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" #if $cdnas.filter_cdnas ---filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}" +--filter-cdnas-output "${fasta_output}" +#end if +#if $cdnas.parse_cdna_names +--parse-cdna-names +#end if +#if $fill_empty +--fill-empty "${fill_empty}" +#end if #end if --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}" ]]></command> @@ -30,6 +37,7 @@ <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/> <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/> <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/> + <param name="fill_empty" type="text" optional='true' value="" label="Column to be used to fill empty values in other fields" help="Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping."/> <conditional name="mito"> <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/> <when value="true"> @@ -39,10 +47,12 @@ <when value="false" /> </conditional> <conditional name="cdnas"> - <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/> + <param name="parse_cdnas" type="boolean" checked="false" label="Provide a cDNA file for extracting annotations and/ or possible filtering?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/> <when value="true"> <param name="fasta_input" type="data" format="fasta,fasta.gz" label="FASTA-format cDNA/ transcript file" /> - <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/> + <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field in GTF to match with sequences."/> + <param name="parse_cdna_names" type="boolean" checked="false" label="Parse the FASTA headers for annotation info?" help="e.g. to find gene IDs for transcripts not present in the GTF. May only work for Ensembl GTFs."/> + <param name="filter_cdnas" type="boolean" checked="false" label="Filter the cDNA file to match the annotations?" /> </when> <when value="false" /> </conditional> @@ -67,9 +77,9 @@ **What it does** -Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. +Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. -You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). +You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). **Inputs** @@ -92,5 +102,6 @@ journal = {GitHub repository}, url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, }</citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </tool> |