| Previous changeset 6:6031247f61d4 (2017-10-28) Next changeset 8:a2bb4f5252a8 (2018-01-28) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830 |
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modified:
diffbind.R diffbind.xml |
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added:
test-data/BT474_ER_1.bam test-data/BT474_ER_1.bed.gz test-data/BT474_ER_2.bam test-data/BT474_ER_2.bed.gz test-data/MCF7_ER_1.bam test-data/MCF7_ER_1.bed.gz test-data/MCF7_ER_2.bam test-data/MCF7_ER_2.bed.gz test-data/out_binding.matrix test-data/out_diffbind.bed |
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removed:
diffbind.tar.bz2 |
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| diff -r 6031247f61d4 -r 681dedc42aca diffbind.R --- a/diffbind.R Sat Oct 28 12:53:58 2017 -0400 +++ b/diffbind.R Sun Jan 28 04:26:11 2018 -0500 |
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| @@ -3,7 +3,11 @@ # 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'); +suppressPackageStartupMessages({ + library('getopt') + library('DiffBind') +}) + options(stringAsfactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) @@ -15,7 +19,9 @@ 'outfile' , 'o', 1, "character", 'plots' , 'p', 2, "character", 'infile' , 'i', 1, "character", - 'format', 'f', 1, 'character' + 'format', 'f', 1, "character", + 'th', 't', 1, "double", + 'bmatrix', 'b', 0, "logical" ), byrow=TRUE, ncol=4); opt = getopt(spec); @@ -27,13 +33,10 @@ q(status=1); } -library('DiffBind') - if ( !is.null(opt$plots) ) { pdf(opt$plots) } - sample = dba(sampleSheet=opt$infile, peakFormat='bed') sample_count = dba.count(sample) sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2) @@ -44,6 +47,11 @@ resSorted <- diff_bind[order(diff_bind$FDR),] write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE) +# Output binding affinity scores +if (!is.null(opt$bmatrix)) { + bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) + write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE) +} dev.off() sessionInfo() |
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| diff -r 6031247f61d4 -r 681dedc42aca diffbind.tar.bz2 |
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| diff -r 6031247f61d4 -r 681dedc42aca diffbind.xml --- a/diffbind.xml Sat Oct 28 12:53:58 2017 -0400 +++ b/diffbind.xml Sun Jan 28 04:26:11 2018 -0500 |
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| b'@@ -1,8 +1,10 @@\n-<tool id="diffbind" name="DiffBind" version="2.2.2">\n+<tool id="diffbind" name="DiffBind" version="2.6.5.0">\n <description> differential binding analysis of ChIP-Seq peak data</description>\n <requirements>\n- <requirement type="package" version="2.0.9">bioconductor-diffbind</requirement>\n+ <requirement type="package" version="2.6.5">bioconductor-diffbind</requirement>\n <requirement type="package" version="1.20.0">r-getopt</requirement>\n+ <!--added rmysql requirement to remove: "Warning: namespace \xe2\x80\x98RMySQL\xe2\x80\x99 is not available"-->\n+ <requirement type="package" version="0.10.11">r-rmysql</requirement>\n </requirements>\n <stdio>\n <regex match="Execution halted"\n@@ -18,8 +20,10 @@\n level="fatal"\n description="An undefined error occured, please check your intput carefully and contact your administrator." />\n </stdio>\n- <command>\n-<![CDATA[\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\\$otherPkgs\\$DiffBind\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")," getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\\$otherPkgs\\$getopt\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rmysql version" $(R --vanilla --slave -e "library(rmysql); cat(sessionInfo()\\$otherPkgs\\$rmysql\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ <command><![CDATA[\n ## seems that diffbind also needs file extensions to work properly\n #set $counter = 1\n #for $sample in $samples:\n@@ -32,15 +36,20 @@\n #set $counter = $counter + 1\n #end for\n \n- Rscript $__tool_directory__/diffbind.R\n+ Rscript \'$__tool_directory__/diffbind.R\'\n -i $infile\n- -o $outfile\n- -p $plots\n+ -o \'$outfile\'\n+ -p \'$plots\'\n -f $format\n+ -t $th\n+\n+ #if $binding_affinity_matrix:\n+ -b\n+ #end if\n ]]>\n </command>\n <configfiles>\n-<configfile name="infile">\n+<configfile name="infile"><![CDATA[\n #set $counter = 1\n #for $sample in $samples:\n #if str( $sample.bamcontrol ) != \'None\' and $counter == 1:\n@@ -54,8 +63,7 @@\n $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + \'_bamreads.bam\'#,$sample.peaks\n #end if\n #set $counter = $counter + 1\n-#end for\n-</configfile>\n+#end for]]></configfile>\n </configfiles>\n <inputs>\n <repeat name="samples" title="Samples" min="2">\n@@ -64,62 +72,326 @@\n <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />\n <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />\n <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />\n- <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>\n- <param format="bam" name="bamcontrol" type="data" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>\n- <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>\n+ <param name="bamreads" type="data" format="bam" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>\n+ <param name="bamcontrol" type="data" format="bam" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>\n+ <param name="peaks" type="data" format="bed" label="Peak file" help="Result of your Peak calling experiment."/>\n </repeat>\n'..b' and reporting\n+\n \n-DiffBind_ Authors: Rory Stark, Gordon Brown (2011)\n+ * **Reading in peaksets**: \n+\n+The first step is to read in a set of peaksets and associated\n+metadata. Peaksets are derived either from ChIP-Seq peak callers, such as MACS\n+([1]), or using some other criterion (e.g. genomic windows, or all the promoter regions\n+in a genome). The easiest way to read in peaksets is using a comma-separated value\n+(csv) sample sheet with one line for each peakset. (Spreadsheets in Excel\xc2\xae format, with\n+a .xls or .xlsx suffix, are also accepted.) A single experiment can have more than\n+one associated peakset; e.g. if multiple peak callers are used for comparison purposes\n+each sample would have more than one line in the sample sheet. Once the peaksets\n+are read in, a merging function finds all overlapping peaks and derives a single set of\n+unique genomic intervals covering all the supplied peaks (a consensus peakset for the\n+experiment).\n+\n+ * **Occupancy analysis**: \n+\n+Peaksets, especially those generated by peak callers, provide\n+an insight into the potential occupancy of the protein being ChIPed for at specific\n+genomic loci. After the peaksets have been loaded, it can be useful to perform some\n+exploratory plotting to determine how these occupancy maps agree with each other,\n+e.g. between experimental replicates (re-doing the ChIP under the same conditions),\n+between different peak callers on the same experiment, and within groups of samples\n+representing a common experimental condition. DiffBind provides functions to enable\n+overlaps to be examined, as well as functions to determine how well similar samples\n+cluster together. Beyond quality control, the product of an occupancy analysis may be\n+a consensus peakset, representing an overall set of candidate binding sites to be used\n+in further analysis.\n+\n+ * **Counting reads**: \n \n-.. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html\n+Once a consensus peakset has been derived, DiffBind can use the\n+supplied sequence read files to count how many reads overlap each interval for each\n+unique sample. The peaks in the consensus peakset may be re-centered and trimmed\n+based on calculating their summits (point of greatest read overlap) in order to provide\n+more standardized peak intervals. The final result of counting is a binding affinity matrix\n+containing a (normalized) read count for each sample at every potential binding site.\n+With this matrix, the samples can be re-clustered using affinity, rather than occupancy,\n+data. The binding affinity matrix is used for QC plotting as well as for subsequent\n+differential analysis.\n+\n+ * **Differential binding affinity analysis**: \n \n+The core functionality of DiffBind is the\n+differential binding affinity analysis, which enables binding sites to be identified that\n+are statistically significantly differentially bound between sample groups. To accomplish\n+this, first a contrast (or contrasts) is established, dividing the samples into groups to\n+be compared. Next the core analysis routines are executed, by default using DESeq2 .\n+This will assign a p-value and FDR to each candidate binding site indicating confidence\n+that they are differentially bound.\n+\n+ * **Plotting and reporting**: \n+\n+Once one or more contrasts have been run, DiffBind provides\n+a number of functions for reporting and plotting the results. MA plots give an\n+overview of the results of the analysis, while correlation heatmaps and PCA plots show\n+how the groups cluster based on differentially bound sites. Boxplots show the distribution\n+of reads within differentially bound sites corresponding to whether they gain or\n+lose affinity between the two sample groups. A reporting mechanism enables differentially\n+bound sites to be extracted for further processing, such as annotation, motif, and\n+pathway analyses.\n+\n+**References**\n+\n+DiffBind Authors: Rory Stark, Gordon Brown (2011)\n Wrapper authors: Bjoern Gruening, Pavankumar Videm\n \n ]]>\n' |
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| diff -r 6031247f61d4 -r 681dedc42aca test-data/out_binding.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_binding.matrix Sun Jan 28 04:26:11 2018 -0500 |
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| b'@@ -0,0 +1,1394 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|
| b |
| diff -r 6031247f61d4 -r 681dedc42aca test-data/out_diffbind.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_diffbind.bed Sun Jan 28 04:26:11 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +chr18 394600 396513 1914 * 7.15 7.89 5.55 2.35 7.06e-24 9.84e-21 +chr18 111567 112005 439 * 5.71 3.63 6.53 -2.89 1.27e-08 8.88e-06 +chr18 346464 347342 879 * 5 3.24 5.77 -2.52 6.51e-06 0.00303 +chr18 399014 400382 1369 * 7.62 8.05 7 1.04 1.04e-05 0.00364 +chr18 371110 372102 993 * 4.63 5.36 3.07 2.3 8.1e-05 0.0226 |