# HG changeset patch
# User pavanvidem
# Date 1432296925 14400
# Node ID 095c44c4603201e6437d9eb3d49597d244d7211e
Uploaded
diff -r 000000000000 -r 095c44c46032 diffbind.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/diffbind.R Fri May 22 08:15:25 2015 -0400
@@ -0,0 +1,49 @@
+## 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")
+
+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(
+ 'verbose', 'v', 2, "integer",
+ 'help' , 'h', 0, "logical",
+ 'outfile' , 'o', 1, "character",
+ 'plots' , 'p', 2, "character",
+ 'infile' , 'i', 1, "character",
+ 'format', 'f', 1, '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$help) ) {
+ cat(getopt(spec, usage=TRUE));
+ q(status=1);
+}
+
+library('DiffBind')
+
+if ( !is.null(opt$plots) ) {
+ pdf(opt$plots)
+}
+
+
+sample = dba(sampleSheet=opt$infile, peakFormat='bed')
+sample_count = dba.count(sample)
+sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
+sample_analyze = dba.analyze(sample_contrast)
+diff_bind = dba.report(sample_analyze)
+orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
+
+resSorted <- diff_bind[order(diff_bind$FDR),]
+write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)
+
+
+dev.off()
+sessionInfo()
diff -r 000000000000 -r 095c44c46032 diffbind.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/diffbind.xml Fri May 22 08:15:25 2015 -0400
@@ -0,0 +1,105 @@
+
+ differential binding analysis of ChIP-Seq peak data
+
+ Rscript
+ DESeq2
+ R
+ deseq2
+ diffbind
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+SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
+#set $counter = 1
+#for $sample in $samples:
+$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
+#set $counter = $counter + 1
+#end for
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+ pdf == True
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diff -r 000000000000 -r 095c44c46032 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri May 22 08:15:25 2015 -0400
@@ -0,0 +1,42 @@
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+ http://www.bioconductor.org/packages/release/bioc/src/contrib/DiffBind_1.14.4.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/IRanges_1.20.6.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/XVector_0.2.0.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/limma_3.18.9.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/gtools_3.1.1.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/gdata_2.13.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/bitops_1.0-6.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/caTools_1.16.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/Biostrings_2.30.1.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/GenomicRanges_1.14.4.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/RColorBrewer_1.0-5.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/amap_0.8-7.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/edgeR_3.4.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/gplots_2.12.1.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/zlibbioc_1.8.0.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/Rsamtools_1.14.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/DiffBind_1.8.3.tar.gz
+ https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/getopt_1.20.0.tar.gz
+
+
+
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+ Differential Binding Analysis of ChIP-Seq peak data
+ http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
+
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+