Mercurial > repos > iuc > dexseq
changeset 5:278b189248cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
| author | iuc |
|---|---|
| date | Mon, 14 Jan 2019 05:02:19 -0500 |
| parents | 251393b72616 |
| children | 9fd8b69e6e68 |
| files | dexseq.R dexseq.xml plotdexseq.R plotdexseq.xml test-data/dexseq.rds test-data/plotdexseq.pdf test-data/plotdexseq_genes.tab test-data/plotdexseq_multi.pdf |
| diffstat | 7 files changed, 169 insertions(+), 5 deletions(-) [+] |
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--- a/dexseq.R Tue Dec 11 00:19:18 2018 -0500 +++ b/dexseq.R Mon Jan 14 05:02:19 2019 -0500 @@ -21,6 +21,7 @@ 'gtf', 'a', 1, "character", 'outfile', 'o', 1, "character", 'reportdir', 'r', 1, "character", + 'rds', 'd', 1, "character", 'factors', 'f', 1, "character", 'threads', 'p', 1, "integer", 'fdr', 'c', 1, "double" @@ -110,10 +111,11 @@ write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) print("Written Results") +if ( !is.null(opt$rds) ) { + saveRDS(res, file="DEXSeqResults.rds") +} + if ( !is.null(opt$reportdir) ) { - save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) - save.image() DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) - unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData")) } sessionInfo()
--- a/dexseq.xml Tue Dec 11 00:19:18 2018 -0500 +++ b/dexseq.xml Mon Jan 14 05:02:19 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> +<tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1"> <description>Determines differential exon usage from count tables</description> <macros> <import>macros.xml</import> @@ -54,6 +54,7 @@ -f '#echo json.dumps(temp_factor_names)#' -a $gtf -c $fdr_cutoff + -d $rds #if $report: -r ./html_out @@ -93,6 +94,8 @@ <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Visualise the analysis results?" help="Output an additional HTML file." /> + <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false" + label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" /> <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/> </inputs> <outputs> @@ -100,6 +103,9 @@ <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}"> <filter>report is True</filter> </data> + <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}"> + <filter>rds is True</filter> + </data> </outputs> <tests> <!-- Ensure default output works--> @@ -151,6 +157,22 @@ <param name="fdr_cutoff" value="0.05"/> <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/> </test> + <!-- Ensure rds output works--> + <test expect_num_outputs="2"> + <param name="gtf" value="dexseq.gtf" ftype="gtf"/> + <repeat name="rep_factorName"> + <param name="factorName" value="condition"/> + <param name="factorLevel1" value="knockdown"/> + <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/> + <param name="factorLevel2" value="control"/> + <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> + </repeat> + <param name="report" value="False"/> + <param name="rds" value="True"/> + <param name="fdr_cutoff" value="0.05"/> + <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/> + <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -188,7 +210,7 @@ **Output** -DEXSeq_ generates a tabular file containing the different columns and an optional html report. +DEXSeq_ generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes. ====== ========================================================== Column Description
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotdexseq.R Mon Jan 14 05:02:19 2019 -0500 @@ -0,0 +1,47 @@ +## Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +# we need that to not crash galaxy with an UTF8 error on German LC settings. +Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library("DEXSeq") + 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( + 'rdata', 'r', 1, "character", + 'primaryfactor', 'p', 1, "character", + 'geneid', 'g', 1, "character", + 'genefile', 'f', 1, "character", + 'fdr', 'c', 1, "double", + 'transcripts', 't', 1, "logical", + 'names', 'a', 1, "logical", + 'normcounts', 'n', 1, "logical", + 'splicing', 's', 1, "logical" +), byrow=TRUE, ncol=4); +opt = getopt(spec); + +res <- readRDS(opt$rdata) + +if (!is.null(opt$genefile)) { + genes <- read.delim(opt$genefile, header=FALSE) + genes <- genes[, 1] +} else { + genes <- opt$geneid +} + +pdf("plot.pdf") +for (i in genes){ + plotDEXSeq(res, i, FDR=opt$fdr, fitExpToVar=opt$primaryfactor, + norCounts=opt$normcounts, expression=TRUE, splicing=opt$splicing, + displayTranscripts=opt$transcripts, names=opt$names, legend=TRUE, + color=NULL, color.samples=NULL, transcriptDb=NULL) +} +dev.off() + +sessionInfo() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotdexseq.xml Mon Jan 14 05:02:19 2019 -0500 @@ -0,0 +1,90 @@ +<tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.0"> + <description>Visualization of the per gene DEXSeq results</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.20.2">r-getopt</requirement> + </expand> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")" + ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ +Rscript '$__tool_directory__/plotdexseq.R' + -r '$rdata' + -p '$primaryfactor' + #if $genes.genes_select == 'list': + -f '$genes.genefile' + #else: + -g '$genes.geneid' + #end if + -c $fdr_cutoff + -t $transcripts + -a $names + -n $normcounts + -s $splicing + ]]></command> + <inputs> + <param name="rdata" type="data" format="rdata" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/> + <param name="primaryfactor" type="text" value="FactorName" label="Specify the primary factor name in the DEXSeqResults object" help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <conditional name="genes"> + <param name="genes_select" type="select" label="Genes to plot" help="Select to input a single gene ID or a list of IDs. Default: single gene ID"> + <option value="single" selected="True">single</option> + <option value="list">list</option> + </param> + <when value="single"> + <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + </when> + <when value="list"> + <param name="genefile" type="data" format="tabular" label="List of gene IDs" help="This should be a single tabular column with one gene per row and no header." /> + </when> + </conditional> + <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/> + <param name="transcripts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcripts" help="If Yes, the transcripts are displayed in the plot. Default: No"/> + <param name="names" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcript names" help="If Yes, the names of the transcripts are shown. Default: No"/> + <param name="normcounts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot count values from the individual samples" help="If yes, provides a plot of the counts normalized by the size factors. Default: No"/> + <param name="splicing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot exon usage" help="If yes, the samples gene expression effects are averaged out, leaving only exon usage coefficients. Default: No" /> + </inputs> + + <outputs> + <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <!-- Ensure default output works--> + <test expect_num_outputs="1"> + <param name="rdata" ftype="rdata" value="dexseq.rds"/> + <param name="primaryfactor" value="condition"/> + <param name="geneid" value="FBgn0000053"/> + <param name="fdr_cutoff" value="1"/> + <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/> + </test> + <!-- Ensure plotting multiple genes works--> + <test expect_num_outputs="1"> + <param name="rdata" ftype="rdata" value="dexseq.rds"/> + <param name="primaryfactor" value="condition"/> + <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> + <param name="fdr_cutoff" value="1"/> + <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool enables visualization of DEXSeq results for individual genes. The input is a DEXSeqResults rds file, which can be output from the DEXSeq tool, and a single gene ID or list of IDs to plot. + +.. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html + ]]></help> + <citations> + <citation type="doi">10.1101/gr.133744.111</citation> + </citations> +</tool>