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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83 |
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added:
diffbind.R diffbind.xml 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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readme.md |
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| diff -r a2bb4f5252a8 -r 6171163112de diffbind.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diffbind.R Sun Jan 28 05:10:25 2018 -0500 |
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| @@ -0,0 +1,57 @@ +## 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('getopt') + library('DiffBind') +}) + +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", + 'th', 't', 1, "double", + 'bmatrix', 'b', 0, "logical" +), 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$help) ) { + cat(getopt(spec, usage=TRUE)); + q(status=1); +} + +if ( !is.null(opt$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) + +# 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 a2bb4f5252a8 -r 6171163112de diffbind.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diffbind.xml Sun Jan 28 05:10:25 2018 -0500 |
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| b'@@ -0,0 +1,402 @@\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="2.6.5">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+ source="both"\n+ level="fatal"\n+ description="Execution halted." />\n+ <regex match="Input-Error 01"\n+ source="both"\n+ level="fatal"\n+ description="Error in your input parameters: Make sure you only apply factors to selected samples." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ </stdio>\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+ ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&\n+ ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&\n+ #if str( $sample.bamcontrol ) != \'None\':\n+ ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&\n+ ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&\n+ #end if\n+ #set $counter = $counter + 1\n+ #end for\n+\n+ Rscript \'$__tool_directory__/diffbind.R\'\n+ -i $infile\n+ -o \'$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"><![CDATA[\n+#set $counter = 1\n+#for $sample in $samples:\n+#if str( $sample.bamcontrol ) != \'None\' and $counter == 1:\n+SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks\n+#elif $counter == 1:\n+SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks\n+#end if\n+#if str( $sample.bamcontrol ) != \'None\':\n+$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + \'_bamreads.bam\'#,#echo str($counter) + \'_bamcontrol.bam\'#,$sample.peaks\n+#else:\n+$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]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <repeat name="samples" title="Samples" min="2">\n+ <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />\n+ <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />\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" valu'..b's\n+ #. Plotting and reporting\n+\n+\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+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+ </help>\n+ <citations>\n+ <citation type="doi">doi:10.1038/nature10730</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r a2bb4f5252a8 -r 6171163112de readme.md --- a/readme.md Sun Jan 28 04:56:33 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -IUC has taken over -================== - -The DiffBind wrapper is now located under https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind. Maintenance and development will happen under the IUC umbrella! |
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| diff -r a2bb4f5252a8 -r 6171163112de test-data/out_binding.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_binding.matrix Sun Jan 28 05:10:25 2018 -0500 |
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| b'@@ -0,0 +1,1394 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|
| b |
| diff -r a2bb4f5252a8 -r 6171163112de test-data/out_diffbind.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_diffbind.bed Sun Jan 28 05:10:25 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 |