Mercurial > repos > pavanvidem > dexseq
changeset 15:b7e9bf50295c draft
Uploaded
author | pavanvidem |
---|---|
date | Tue, 01 Sep 2015 08:19:08 -0400 |
parents | a6949dd64d9c |
children | 33c17175e3d6 |
files | dexseq.R dexseq.xml tool_dependencies.xml |
diffstat | 3 files changed, 30 insertions(+), 17 deletions(-) [+] |
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--- a/dexseq.R Mon Aug 31 09:51:13 2015 -0400 +++ b/dexseq.R Tue Sep 01 08:19:08 2015 -0400 @@ -18,14 +18,20 @@ 'help', 'h', 0, "logical", 'gtf', 'a', 1, "character", 'outfile', 'o', 1, "character", - 'report', 'r', 1, "character", + 'reportdir', 'r', 1, "character", + 'htmlfile', 'x', 1, "character", 'factors', 'f', 1, "character", 'threads', 'p', 1, "integer", - 'fdr', 'c', 1, "double", + 'fdr', 'c', 1, "double" ), byrow=TRUE, ncol=4); opt = getopt(spec); -setwd(opt$report) + +#reportdir <- gsub(".dat", "_files", opt$outfile) + +dir.create(file.path(opt$reportdir)) +setwd(opt$reportdir) +getwd() # if help was asked for print a friendly message # and exit with a non-zero error code @@ -79,8 +85,9 @@ formulaReducedModel primaryFactor countFiles -opt$report -file.path(opt$report,"DEXSeq_analysis.RData") +opt$reportdir +opt$htmlfile +opt$threads getwd() dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf) @@ -97,12 +104,14 @@ resSorted <- res[order(res$padj),] head(resSorted) -write.csv(as.data.frame(resSorted), file=opt$outfile) +write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) -if ( !is.null(opt$report) ) { - save(dxd, resSorted, file = file.path(opt$report,"DEXSeq_analysis.RData")) +if ( !is.null(opt$reportdir) ) { + save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) save.image() - DEXSeqHTML(res, FDR=opt$fdr, color=c("#C3EEE7","#B7FEA0","#F1E7A1","#CEAEFF","#FF8F43","#EDC3C5","#AAA8AA","#FF0000","#637EE9","#FBFBFB"), BPPARAM=BPPARAM) - unlink(file.path(opt$report,"DEXSeq_analysis.RData")) + DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#C3EEE7","#B7FEA0","#F1E7A1","#CEAEFF","#FF8F43","#EDC3C5","#AAA8AA","#FF0000","#637EE9","#FBFBFB")) + unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData")) } +file.remove(opt$htmlfile) +file.symlink(file.path(opt$reportdir,"testForDEU.html"), opt$htmlfile) sessionInfo()
--- a/dexseq.xml Mon Aug 31 09:51:13 2015 -0400 +++ b/dexseq.xml Tue Sep 01 08:19:08 2015 -0400 @@ -1,5 +1,5 @@ <tool id="dexseq" name="DEXSeq" version="1.0"> - <description>Determines differentially expressed features from count tables</description> + <description>Determines differential exon usage from count tables</description> <requirements> <requirement type="package" version="3.2.0">R</requirement> <requirement type="binary">Rscript</requirement> @@ -9,7 +9,7 @@ <command> #import json Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/pavanvidem/dexseq/cbd118202fd1/dexseq/dexseq.R - #set $reportdir = $dexseq_out.files_path + #set $reportdir = str($dexseq_out).replace('.dat','_files') -o "$dexseq_out" -p 12 #set $temp_factor_names = list() @@ -27,9 +27,12 @@ -f '#echo json.dumps(temp_factor_names)#' -a $gtf #if $report: - -p "$reportdir" + -x "$htmlreport" + -r "$reportdir" #end if - -c $fdr_cutoff + -c $fdr_cutoff; + +## cp #echo os.path.join($reportdir, 'testForDEU.html')# $htmlreport; </command> <stdio> <regex match="Execution halted" @@ -71,9 +74,9 @@ </inputs> <outputs> - <data format="tabular" name="dexseq_out" label="DESeq2 result file on ${on_string}"/> - <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> - <filter>pdf == True</filter> + <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/> + <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> + <filter>report == True</filter> </data> </outputs> <code file="dexseq_helper.py" />
--- a/tool_dependencies.xml Mon Aug 31 09:51:13 2015 -0400 +++ b/tool_dependencies.xml Tue Sep 01 08:19:08 2015 -0400 @@ -10,6 +10,7 @@ <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="R" version="3.2.0" /> </repository> + <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Cairo_1.5-8.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/rjson_0.2.15.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/getopt_1.20.0.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/lambda.r_1.1.7.tar.gz</package>