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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 7d5f48c98d81dea756bc3d0b5705c8989c1eb204 |
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added:
readme.md |
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removed:
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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| diff -r 681dedc42aca -r a2bb4f5252a8 diffbind.R --- a/diffbind.R Sun Jan 28 04:26:11 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,57 +0,0 @@ -## 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 681dedc42aca -r a2bb4f5252a8 diffbind.xml --- a/diffbind.xml Sun Jan 28 04:26:11 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,402 +0,0 @@\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 681dedc42aca -r a2bb4f5252a8 readme.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Sun Jan 28 04:56:33 2018 -0500 |
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| @@ -0,0 +1,4 @@ +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 681dedc42aca -r a2bb4f5252a8 test-data/out_binding.matrix --- a/test-data/out_binding.matrix Sun Jan 28 04:26:11 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1394 +0,0 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-chr18\t74826803\t74827698\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74850113\t74850847\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74967232\t74968167\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74974177\t74975856\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75162079\t75162656\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75306150\t75306689\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75404862\t75405830\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75463876\t75464359\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76166820\t76167943\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76212084\t76212732\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76244283\t76244913\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76247276\t76247878\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76355382\t76355883\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76382039\t76382699\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76398929\t76399745\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76431621\t76432094\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76528540\t76529917\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76533867\t76534686\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76566546\t76567310\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76574330\t76575226\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76652675\t76653264\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76653336\t76654222\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76734601\t76735073\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76749882\t76750469\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76759894\t76760344\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76822532\t76823743\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77062037\t77062828\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77173663\t77174478\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77300430\t77301170\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77424530\t77425198\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77438941\t77440103\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77541065\t77541645\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77694136\t77695082\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77725047\t77725936\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77968049\t77968792\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77987486\t77988208\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n' |
| b |
| diff -r 681dedc42aca -r a2bb4f5252a8 test-data/out_diffbind.bed --- a/test-data/out_diffbind.bed Sun Jan 28 04:26:11 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -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 |