| Next changeset 1:e25d81465c23 (2023-10-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d |
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added:
macros.xml ribowaltz.R ribowaltz_plot.R ribowaltz_plot.xml test-data/rep1.bam test-data/rep1.rdata test-data/rep1_annot.gtf.gz |
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| diff -r 000000000000 -r 8e903cb3f919 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Sep 22 20:30:20 2022 +0000 |
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| @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2.0">ribowaltz</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@PROFILE@">21.05</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_4027</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0439</edam_operation> + </edam_operations> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1006169</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>riboWaltz</xref> + </xrefs> + </xml> +</macros> |
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| diff -r 000000000000 -r 8e903cb3f919 ribowaltz.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribowaltz.R Thu Sep 22 20:30:20 2022 +0000 |
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| @@ -0,0 +1,131 @@ +# setup R error handling to go to stderr +options(show.error.messages = FALSE, error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) +}) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +library("getopt") +options(stringAsFactors = FALSE, useFancyQuotes = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). +spec <- matrix(c( + "quiet", "q", 0, "logical", + "help", "h", 0, "logical", + "bamdir", "b", 1, "character", + "gtffile", "g", 1, "character", + "codon_coverage_info", "Y", 1, "character", + "cds_coverage_info", "Z", 1, "character", + "psite_info_rdata", "O", 0, "character", + "refseq_sep", "s", 0, "character", + "params_duplicate_filterting", "d", 0, "character", + "params_peridiocity_filterting", "l", 0, "character", + "params_custom_filterting", "c", 0, "character", + "params_psite_additional", "p", 0, "character", + "params_coverage_additional", "C", 0, "character" +), byrow = TRUE, ncol = 4) +opt <- getopt(spec) + +# if help was asked for print a friendly message +# and exit with a non-zero error code +if (!is.null(opt$help)) { + cat(getopt(spec, usage = TRUE)) + q(status = 1) +} + +verbose <- is.null(opt$quiet) + +library("riboWaltz") + +# create annotation data table +annotation_dt <- create_annotation(opt$gtffile) + +sep <- opt$refseq_sep +if (opt$refseq_sep == "") { + sep <- NULL +} +# convert alignments in BAM files into list of data tables +reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep) + +library("jsonlite") +# remove duplicate reads +if (!is.null(opt$params_duplicate_filterting)) { + json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting) + reads_list <- duplicates_filter( + data = reads_list, + extremity = json_duplicate_filterting$extremity, + keep = json_duplicate_filterting$keep + ) +} + +# selection of read lengths - periodicity filtering +if (!is.null(opt$params_peridiocity_filterting)) { + json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting) + reads_list <- length_filter( + data = reads_list, + length_filter_mode = "periodicity", + periodicity_threshold = json_peridiocity_filterting$periodicity_threshold + ) +} +# selection of read lengths - length range filtering +if (!is.null(opt$params_custom_filterting)) { + json_custom_filterting <- fromJSON(opt$params_custom_filterting) + reads_list <- length_filter( + data = reads_list, + length_filter_mode = "custom", + length_range = json_custom_filterting$length_range + ) +} + +# compute P-site offset +json_psite_additional <- fromJSON(opt$params_psite_additional) +psite_offset <- psite( + reads_list, + start = json_psite_additional$use_start, + flanking = json_psite_additional$flanking, + extremity = json_psite_additional$psite_extrimity, + plot = TRUE, + cl = json_psite_additional$cl, + plot_format = "pdf", + plot_dir = "plots" +) +psite_offset + +reads_psite_list <- psite_info(reads_list, psite_offset) +reads_psite_list +# write a separate P-site offset info table for each sample +for (sample in names(reads_psite_list)) { + write.table( + reads_psite_list[[sample]], + file = paste(sample, "psite_info.tsv", sep = "_"), + sep = "\t", row.names = FALSE, quote = FALSE + ) + print(paste(sample, "psite_info.tsv", sep = "_")) +} + +# write R object to a file +if (!is.null(opt$psite_info_rdata)) { + save(reads_psite_list, annotation_dt, file = opt$psite_info_rdata) +} + +json_coverage_additional <- fromJSON(opt$params_coverage_additional) +# codon coverage +codon_coverage_out <- codon_coverage( + reads_psite_list, + annotation_dt, + psite = json_coverage_additional$psites_per_region, + min_overlap = json_coverage_additional$min_overlap +) +write.table(codon_coverage_out, file = opt$codon_coverage_info, sep = "\t", row.names = FALSE, quote = FALSE) + +# CDS coverage +cds_coverage_out <- cds_coverage( + reads_psite_list, + annotation_dt, + start_nts = json_coverage_additional$start_nts, + stop_nts = json_coverage_additional$stop_nts +) +write.table(cds_coverage_out, file = opt$cds_coverage_info, sep = "\t", row.names = FALSE, quote = FALSE) |
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| diff -r 000000000000 -r 8e903cb3f919 ribowaltz_plot.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribowaltz_plot.R Thu Sep 22 20:30:20 2022 +0000 |
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| @@ -0,0 +1,152 @@ +# setup R error handling to go to stderr +options(show.error.messages = FALSE, error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) +}) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +library("getopt") +options(stringAsFactors = FALSE, useFancyQuotes = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). +spec <- matrix(c( + "quiet", "q", 0, "logical", + "help", "h", 0, "logical", + "input_rdata", "i", 1, "character", + "params_rlength_distr", "r", 0, "character", + "params_rends_heat", "e", 0, "character", + "region_psite_plot", "R", 0, "logical", + "params_trint_periodicity", "t", 0, "character", + "params_metaplots", "m", 0, "character", + "params_codon_usage_psite", "u", 0, "character" +), byrow = TRUE, ncol = 4) +opt <- getopt(spec) + +# if help was asked for print a friendly message +# and exit with a non-zero error code +if (!is.null(opt$help)) { + cat(getopt(spec, usage = TRUE)) + q(status = 1) +} + +verbose <- is.null(opt$quiet) + +library("riboWaltz") +library("jsonlite") + +load(opt$input_rdata) + +if (!is.null(opt$params_rlength_distr)) { + pdf("read_lengths.pdf") + json_rlength_distr <- fromJSON(opt$params_rlength_distr) + length_dist <- rlength_distr( + reads_psite_list, + sample = names(reads_psite_list), + cl = json_rlength_distr$cl, + multisamples = json_rlength_distr$multisamples, + plot_style = json_rlength_distr$plot_style + ) + print(length_dist) + dev.off() +} + +if (!is.null(opt$params_rends_heat)) { + pdf("read_ends_heatmap.pdf", height = 5 * length(reads_psite_list), width = 15) + json_rends_heat <- fromJSON(opt$params_rends_heat) + for (sample_name in names(reads_psite_list)) { + ends_heatmap <- rends_heat( + reads_psite_list, + annotation_dt, + sample = sample_name, + cl = json_rends_heat$cl, + utr5l = json_rends_heat$utr5l, + cdsl = json_rends_heat$cdsl, + utr3l = json_rends_heat$utr3l + ) + print(ends_heatmap[["plot"]]) + } + dev.off() +} + +if (!is.null(opt$region_psite_plot)) { + pdf("psites_per_region.pdf", height = 12, width = 7 * length(reads_psite_list)) + psite_region <- region_psite(reads_psite_list, annotation_dt, sample = names(reads_psite_list)) + print(psite_region[["plot"]]) + dev.off() +} + +if (!is.null(opt$params_trint_periodicity)) { + pdf("trinucleotide_periodicity.pdf", height = 6 * length(reads_psite_list), width = 10) + json_trint_periodicity <- fromJSON(opt$params_trint_periodicity) + frames_stratified <- frame_psite_length( + reads_psite_list, + sample = names(reads_psite_list), + cl = json_trint_periodicity$cl, + region = json_trint_periodicity$region, + length_range = json_trint_periodicity$length_range + ) + frames_stratified[["plot"]] + frames <- frame_psite_length( + reads_psite_list, + sample = names(reads_psite_list), + region = json_trint_periodicity$region, + length_range = json_trint_periodicity$length_range + ) + print(frames[["plot"]]) + dev.off() +} + +if (!is.null(opt$params_metaplots)) { + pdf("metaplots.pdf", height = 5 * length(reads_psite_list), width = 24) + json_metaplots <- fromJSON(opt$params_metaplots) + metaprofile <- metaprofile_psite( + reads_psite_list, + annotation_dt, + sample = names(reads_psite_list), + multisamples = json_metaplots$multisamples, + plot_style = json_metaplots$plot_style, + length_range = json_metaplots$length_range, + frequency = json_metaplots$frequency, + utr5l = json_metaplots$utr5l, + cdsl = json_metaplots$cdsl, + utr3l = json_metaplots$utr3l, + plot_title = "sample.transcript.length_range" + ) + print(metaprofile) + sample_list <- list() + for (sample_name in names(reads_psite_list)) { + sample_list[[sample_name]] <- c(sample_name) + } + metaheatmap <- metaheatmap_psite( + reads_psite_list, + annotation_dt, + sample = sample_list, + length_range = json_metaplots$length_range, + utr5l = json_metaplots$utr5l, + cdsl = json_metaplots$cdsl, + utr3l = json_metaplots$utr3l, + plot_title = "Comparison metaheatmap" + ) + print(metaheatmap[["plot"]]) + dev.off() +} + +if (!is.null(opt$params_codon_usage_psite)) { + pdf("codon_usage.pdf", height = 6, width = 16) + json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite) + for (sample_name in names(reads_psite_list)) { + cu_barplot <- codon_usage_psite( + reads_psite_list, + annotation_dt, + sample = sample_name, + fastapath = json_codon_usage_psite$fastapath, + fasta_genome = FALSE, + frequency_normalization = json_codon_usage_psite$frequency + ) + print(cu_barplot[["plot"]]) + } + dev.off() +} |
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| diff -r 000000000000 -r 8e903cb3f919 ribowaltz_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribowaltz_plot.xml Thu Sep 22 20:30:20 2022 +0000 |
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| b'@@ -0,0 +1,253 @@\n+<tool id="ribowaltz_plot" name="riboWaltz-plot" version="@VERSION@" profile="@PROFILE@">\n+ <description>visual inspection of ribosome profiling data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'requirements\'/>\n+ <expand macro=\'edam_ontology\' />\n+ <expand macro=\'xrefs\'/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript \'${__tool_directory__}/ribowaltz_plot.R\' -i \'$input_rdata\'\n+ #import json\n+ #if $rlength_distr.plot == \'yes\':\n+ #set params_rlength_distr = []\n+ #silent $params_rlength_distr.append(\n+ {"cl": int($rlength_distr.plot_options.cl), "multisamples": str($rlength_distr.plot_options.multisamples),\n+ "plot_style": str($rlength_distr.plot_options.plot_style)})\n+ --params_rlength_distr \'#echo json.dumps($params_rlength_distr)#\'\n+ #end if\n+ #if $rends_heat.plot == \'yes\':\n+ #set params_rends_heat = []\n+ #silent $params_rends_heat.append(\n+ {"cl": int($rends_heat.plot_options.cl), "utr5l": int($rends_heat.plot_options.utr5l),\n+ "cdsl": int($rends_heat.plot_options.cdsl), "utr3l": int($rends_heat.plot_options.utr3l)})\n+ --params_rends_heat \'#echo json.dumps($params_rends_heat)#\'\n+ #end if\n+ #if $region_psite:\n+ --region_psite_plot\n+ #end if\n+ #if $trint_periodicity.plot == \'yes\':\n+ #set length_range = \'all\' \n+ #if $trint_periodicity.plot_options.length_range.filter == \'range\':\n+ #$length_range = str($trint_periodicity.plot_options.length_range.length_range_min) + \':\' + str($trint_periodicity.plot_options.length_range.length_range_max)\n+ #end if\n+ #set params_trint_periodicity = []\n+ #silent $params_trint_periodicity.append(\n+ {"cl": int($trint_periodicity.plot_options.cl), "region": str($trint_periodicity.plot_options.region), \n+ "length_range": $length_range})\n+ --params_trint_periodicity \'#echo json.dumps($params_trint_periodicity)#\'\n+ #end if\n+ #if $metaplots.plot == \'yes\':\n+ #set length_range = \'all\' \n+ #if $metaplots.plot_options.length_range.filter == \'range\':\n+ #$length_range = str($metaplots.plot_options.length_range.length_range_min) + \':\' + str($metaplots.plot_options.length_range.length_range_max)\n+ #end if\n+ #set params_metaplots = []\n+ #silent $params_metaplots.append(\n+ {"multisamples": str($metaplots.plot_options.multisamples), "plot_style": str($metaplots.plot_options.plot_style),\n+ "length_range": $length_range, "frequency": bool($metaplots.plot_options.frequency),\n+ "utr5l": int($metaplots.plot_options.utr5l), "cdsl": int($metaplots.plot_options.cdsl),\n+ "utr3l": int($metaplots.plot_options.utr3l)})\n+ --params_metaplots \'#echo json.dumps($params_metaplots)#\'\n+ #end if\n+ #if $codon_usage_psite.plot == \'yes\':\n+ #set params_codon_usage_psite = []\n+ #silent $params_codon_usage_psite.append(\n+ {"fastapath": str($codon_usage_psite.plot_options.fastapath), "frequency": bool($codon_usage_psite.plot_options.frequency),\n+ "label_scatter": bool($codon_usage_psite.plot_options.label_scatter),\n+ "label_number": int($codon_usage_psite.plot_options.label_number)})\n+ --params_codon_usage_psite \'#echo json.dumps($params_codon_usage_psite)#\'\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input_rdata" type="data" format="rdata" label="RDATA file generated by riboWaltz tool"/>\n+ <conditional name="rlength_distr">\n+ <param name="plot" type="select" label="Include read length distribution plots?">\n+ <option value="no">no</option>\n+ '..b'tart and stop codon"/>\n+ <param name="utr3l" type="integer" value="25" min="0" label="3\' UTR region flanking the stop codon"/>\n+ </section>\n+ </when>\n+ <when value="no"/>\n+ </conditional>\n+ <conditional name="codon_usage_psite">\n+ <param name="plot" type="select" label="Inlcude plots with codon usage?">\n+ <option value="no">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="yes">\n+ <section name="plot_options" title="Plot options">\n+ <param name="fastapath" type="data" format="fasta" />\n+ <param name="frequency" type="boolean" truevalue="1" falsevalue="0" checked="true"\n+ label="normalize the 64 codon usage indexes for the corresponding codon frequencies in coding sequences?"/>\n+ <param name="label_scatter" type="boolean" truevalue="1" falsevalue="0" checked="false"\n+ label="Label the dots in the scatter plot?"\n+ help=" This parameter is considered only if there exatcly two input samples"/>\n+ <param name="label_number" type="integer" value="64" min="1" max="64" label="how many dots in the scatter plot should be labeled?"/>\n+ </section>\n+ </when>\n+ <when value="no"/>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <collection name="out_plots" type="list" label="riboWaltz plots on ${on_string}">\n+ <discover_datasets pattern="(?P<designation>.+)\\.pdf" format="pdf" directory="." visible="false"/>\n+ </collection>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="input_rdata" value="rep1.rdata"/>\n+ <param name="region_psite" value="1"/>\n+ <conditional name="rlength_distr">\n+ <param name="plot" value="yes"/>\n+ </conditional>\n+ <conditional name="rends_heat">\n+ <param name="plot" value="yes"/>\n+ </conditional>\n+ <conditional name="trint_periodicity">\n+ <param name="plot" value="yes"/>\n+ </conditional>\n+ <conditional name="metaplots">\n+ <param name="plot" value="yes"/>\n+ </conditional>\n+ <output_collection name="out_plots" type="list">\n+ <element name="metaplots">\n+ <assert_contents>\n+ <has_size value="9180" delta="100"/>\n+ </assert_contents>\n+ </element>\n+ <element name="psites_per_region">\n+ <assert_contents>\n+ <has_size value="5187" delta="100"/>\n+ </assert_contents>\n+ </element>\n+ <element name="read_ends_heatmap">\n+ <assert_contents>\n+ <has_size value="26327" delta="500"/>\n+ </assert_contents>\n+ </element>\n+ <element name="read_lengths">\n+ <assert_contents>\n+ <has_size value="4877" delta="100"/>\n+ </assert_contents>\n+ </element>\n+ <element name="trinucleotide_periodicity">\n+ <assert_contents>\n+ <has_size value="7730" delta="100"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Visual inspection of ribosome profiling data. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz\n+\n+**Inputs**\n+\n+RDATA file generated by rioWaltz tool.\n+\n+**Outputs**\n+\n+Generates various plots to visualize P-site offsets, codon usage etc.\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 8e903cb3f919 test-data/rep1_annot.gtf.gz |
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