# HG changeset patch # User kevyin # Date 1356046073 18000 # Node ID d27851e0cbbdcba7d0742ad21825d80243524a1d # Parent 0bc4439da640e3ef453ac75fa1760e18a66053e8 Uploaded diff -r 0bc4439da640 -r d27851e0cbbd README --- a/README Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -Homer wrapper for Galaxy - -The homer tools will need to be accessible from command line - -Code repo: https://bitbucket.org/gvl/homer - -=========================================: -LICENSE for this wrapper: -=========================================: -Kevin Ying -Garvan Institute: http://www.garvan.org.au -GVL: https://genome.edu.au/wiki/GVL - -http://opensource.org/licenses/mit-license.php - diff -r 0bc4439da640 -r d27851e0cbbd annotatePeaks.xml --- a/annotatePeaks.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,164 +0,0 @@ - - - homer - - - - - annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated - 2> $out_log || echo "Error running annotatePeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer annoatePeaks** - - More information on accepted formats and options - - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. - -**Parameter list** - -Command line options (not all of them are supported):: - - Usage: annotatePeaks.pl <peak file | tss> <genome version> [additional options...] - - Available Genomes (required argument): (name,org,directory,default promoter set) - -- or -- - Custom: provide the path to genome FASTA files (directory or single file) - - User defined annotation files (default is UCSC refGene annotation): - annotatePeaks.pl accepts GTF (gene transfer formatted) files to annotate positions relative - to custom annotations, such as those from de novo transcript discovery or Gencode. - -gtf <gtf format file> (-gff and -gff3 can work for those files, but GTF is better) - - Peak vs. tss/tts/rna mode (works with custom GTF file): - If the first argument is "tss" (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric - analysis will be carried out. Tag counts and motifs will be found relative to the TSS. - (no position file needed) ["tts" now works too - e.g. 3' end of gene] - ["rna" specifies gene bodies, will automaticall set "-size given"] - NOTE: The default TSS peak size is 4000 bp, i.e. +/- 2kb (change with -size option) - -list <gene id list> (subset of genes to perform analysis [unigene, gene id, accession, - probe, etc.], default = all promoters) - -cTSS <promoter position file i.e. peak file> (should be centered on TSS) - - Primary Annotation Options: - -mask (Masked repeats, can also add 'r' to end of genome name) - -m <motif file 1> [motif file 2] ... (list of motifs to find in peaks) - -mscore (reports the highest log-odds score within the peak) - -nmotifs (reports the number of motifs per peak) - -mdist (reports distance to closest motif) - -mfasta <filename> (reports sites in a fasta file - for building new motifs) - -fm <motif file 1> [motif file 2] (list of motifs to filter from above) - -rmrevopp <#> (only count sites found within <#> on both strands once, i.e. palindromic) - -matrix <prefix> (outputs a motif co-occurrence files: - prefix.count.matrix.txt - number of peaks with motif co-occurrence - prefix.ratio.matrix.txt - ratio of observed vs. expected co-occurrence - prefix.logPvalue.matrix.txt - co-occurrence enrichment - prefix.stats.txt - table of pair-wise motif co-occurrence statistics - additional options: - -matrixMinDist <#> (minimum distance between motif pairs - to avoid overlap) - -matrixMaxDist <#> (maximum distance between motif pairs) - -mbed <filename> (Output motif positions to a BED file to load at UCSC (or -mpeak)) - -mlogic <filename> (will output stats on common motif orientations) - -d <tag directory 1> [tag directory 2] ... (list of experiment directories to show - tag counts for) NOTE: -dfile <file> where file is a list of directories in first column - -bedGraph <bedGraph file 1> [bedGraph file 2] ... (read coverage counts from bedGraph files) - -wig <wiggle file 1> [wiggle file 2] ... (read coverage counts from wiggle files) - -p <peak file> [peak file 2] ... (to find nearest peaks) - -pdist to report only distance (-pdist2 gives directional distance) - -pcount to report number of peaks within region - -vcf <VCF file> (annotate peaks with genetic variation infomation, one col per individual) - -editDistance (Computes the # bp changes relative to reference) - -individuals <name1> [name2] ... (restrict analysis to these individuals) - -gene <data file> ... (Adds additional data to result based on the closest gene. - This is useful for adding gene expression data. The file must have a header, - and the first column must be a GeneID, Accession number, etc. If the peak - cannot be mapped to data in the file then the entry will be left empty. - -go <output directory> (perform GO analysis using genes near peaks) - -genomeOntology <output directory> (perform genomeOntology analysis on peaks) - -gsize <#> (Genome size for genomeOntology analysis, default: 2e9) - - Annotation vs. Histogram mode: - -hist <bin size in bp> (i.e 1, 2, 5, 10, 20, 50, 100 etc.) - The -hist option can be used to generate histograms of position dependent features relative - to the center of peaks. This is primarily meant to be used with -d and -m options to map - distribution of motifs and ChIP-Seq tags. For ChIP-Seq peaks for a Transcription factor - you might want to use the -center option (below) to center peaks on the known motif - ** If using "-size given", histogram will be scaled to each region (i.e. 0-100%), with - the -hist parameter being the number of bins to divide each region into. - Histogram Mode specific Options: - -nuc (calculated mononucleotide frequencies at each position, - Will report by default if extracting sequence for other purposes like motifs) - -di (calculated dinucleotide frequencies at each position) - -histNorm <#> (normalize the total tag count for each region to 1, where <#> is the - minimum tag total per region - use to avoid tag spikes from low coverage - -ghist (outputs profiles for each gene, for peak shape clustering) - -rm <#> (remove occurrences of same motif that occur within # bp) - - Peak Centering: (other options are ignored) - -center <motif file> (This will re-center peaks on the specified motif, or remove peak - if there is no motif in the peak. ONLY recentering will be performed, and all other - options will be ignored. This will output a new peak file that can then be reanalyzed - to reveal fine-grain structure in peaks (It is advised to use -size < 200) with this - to keep peaks from moving too far (-mirror flips the position) - -multi (returns genomic positions of all sites instead of just the closest to center) - - Advanced Options: - -len <#> / -fragLength <#> (Fragment length, default=auto, might want to set to 0 for RNA) - -size <#> (Peak size[from center of peak], default=inferred from peak file) - -size #,# (i.e. -size -10,50 count tags from -10 bp to +50 bp from center) - -size "given" (count tags etc. using the actual regions - for variable length regions) - -log (output tag counts as log2(x+1+rand) values - for scatter plots) - -sqrt (output tag counts as sqrt(x+rand) values - for scatter plots) - -strand <+|-|both> (Count tags on specific strands relative to peak, default: both) - -pc <#> (maximum number of tags to count per bp, default=0 [no maximum]) - -cons (Retrieve conservation information for peaks/sites) - -CpG (Calculate CpG/GC content) - -ratio (process tag values as ratios - i.e. chip-seq, or mCpG/CpG) - -nfr (report nuclesome free region scores instead of tag counts, also -nfrSize <#>) - -norevopp (do not search for motifs on the opposite strand [works with -center too]) - -noadj (do not adjust the tag counts based on total tags sequenced) - -norm <#> (normalize tags to this tag count, default=1e7, 0=average tag count in all directories) - -pdist (only report distance to nearest peak using -p, not peak name) - -map <mapping file> (mapping between peak IDs and promoter IDs, overrides closest assignment) - -noann, -nogene (skip genome annotation step, skip TSS annotation) - -homer1/-homer2 (by default, the new version of homer [-homer2] is used for finding motifs) - - - - - diff -r 0bc4439da640 -r d27851e0cbbd bed2pos.xml --- a/bed2pos.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - homer - - - - - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - Converts: BED -(to)-> homer peak positions - - **Homer bed2pos.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 0bc4439da640 -r d27851e0cbbd findPeaks.xml --- a/findPeaks.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ - - - homer - - Homer's peakcaller. Requires tag directories (see makeTagDirectory) - - - findPeaks $tagDir.extra_files_path $options -o $outputPeakFile - - #if $control_tagDir: - -i $control_tagDir.extra_files_path - #end if - - 2> $out_log || echo "Error running findPeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer findPeaks** - - For more options, look under: "Command line options for findPeaks" - - http://biowhat.ucsd.edu/homer/ngs/peaks.html - - TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. - -**Parameter list** - -Command line options (not all of them are supported):: - - Usage: findPeaks <tag directory> [options] - - Finds peaks in the provided tag directory. By default, peak list printed to stdout - - General analysis options: - -o <filename|auto> (file name for to output peaks, default: stdout) - "-o auto" will send output to "<tag directory>/peaks.txt", ".../regions.txt", - or ".../transcripts.txt" depending on the "-style" option - -style <option> (Specialized options for specific analysis strategies) - factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt, default) - histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt) - groseq (de novo transcript identification from GroSeq data, transcripts.txt) - tss (TSS identification from 5' RNA sequencing, tss.txt) - dnase (Hypersensitivity [crawford style (nicking)], peaks.txt) - - chipseq/histone options: - -i <input tag directory> (Experiment to use as IgG/Input/Control) - -size <#> (Peak size, default: auto) - -minDist <#> (minimum distance between peaks, default: peak size x2) - -gsize <#> (Set effective mappable genome size, default: 2e9) - -fragLength <#|auto> (Approximate fragment length, default: auto) - -inputFragLength <#|auto> (Approximate fragment length of input tags, default: auto) - -tbp <#> (Maximum tags per bp to count, 0 = no limit, default: auto) - -inputtbp <#> (Maximum tags per bp to count in input, 0 = no limit, default: auto) - -strand <both|separate> (find peaks using tags on both strands or separate, default:both) - -norm # (Tag count to normalize to, default 10000000) - -region (extends start/stop coordinates to cover full region considered "enriched") - -center (Centers peaks on maximum tag overlap and calculates focus ratios) - -nfr (Centers peaks on most likely nucleosome free region [works best with mnase data]) - (-center and -nfr can be performed later with "getPeakTags" - - Peak Filtering options: (set -F/-L/-C to 0 to skip) - -F <#> (fold enrichment over input tag count, default: 4.0) - -P <#> (poisson p-value threshold relative to input tag count, default: 0.0001) - -L <#> (fold enrichment over local tag count, default: 4.0) - -LP <#> (poisson p-value threshold relative to local tag count, default: 0.0001) - -C <#> (fold enrichment limit of expected unique tag positions, default: 2.0) - -localSize <#> (region to check for local tag enrichment, default: 10000) - -inputSize <#> (Size of region to search for control tags, default: 2x peak size) - -fdr <#> (False discovery rate, default = 0.001) - -poisson <#> (Set poisson p-value cutoff, default: uses fdr) - -tagThreshold <#> (Set # of tags to define a peak, default: 25) - -ntagThreshold <#> (Set # of normalized tags to define a peak, by default uses 1e7 for norm) - -minTagThreshold <#> (Absolute minimum tags per peak, default: expected tags per peak) - - GroSeq Options: (Need to specify "-style groseq"): - -tssSize <#> (size of region for initiation detection/artifact size, default: 250) - -minBodySize <#> (size of regoin for transcript body detection, default: 1000) - -maxBodySize <#> (size of regoin for transcript body detection, default: 10000) - -tssFold <#> (fold enrichment for new initiation dectection, default: 4.0) - -bodyFold <#> (fold enrichment for new transcript dectection, default: 4.0) - -endFold <#> (end transcript when levels are this much less than the start, default: 10.0) - -fragLength <#> (Approximate fragment length, default: 150) - -uniqmap <directory> (directory of binary files specifying uniquely mappable locations) - Download from http://biowhat.ucsd.edu/homer/groseq/ - -confPvalue <#> (confidence p-value: 1.00e-05) - -minReadDepth <#> (Minimum initial read depth for transcripts, default: auto) - -pseudoCount <#> (Pseudo tag count, default: 2.0) - -gtf <filename> (Output de novo transcripts in GTF format) - "-o auto" will produce <dir>/transcripts.txt and <dir>/transcripts.gtf - - - diff -r 0bc4439da640 -r d27851e0cbbd makeTagDirectory.py --- a/makeTagDirectory.py Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -""" - - -""" -import re -import os -import sys -import subprocess -import optparse -import shutil -import tempfile - -def getFileString(fpath, outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath, fpath) - s = '? ?' - if os.path.isfile(fp): - n = float(os.path.getsize(fp)) - if n > 2**20: - size = ' (%1.1f MB)' % (n/2**20) - elif n > 2**10: - size = ' (%1.1f KB)' % (n/2**10) - elif n > 0: - size = ' (%d B)' % (int(n)) - s = '%s %s' % (fpath, size) - return s - -class makeTagDirectory(): - """wrapper - """ - - def __init__(self,opts=None, args=None): - self.opts = opts - self.args = args - - def run_makeTagDirectory(self): - """ - makeTagDirectory [options] [alignment file 2] - - """ - if self.opts.format != "bam": - cl = [self.opts.executable] + args + ["-format" , self.opts.format] - else: - cl = [self.opts.executable] + args - print cl - p = subprocess.Popen(cl) - retval = p.wait() - - - html = self.gen_html(args[0]) - #html = self.gen_html() - return html,retval - - def gen_html(self, dr=os.getcwd()): - flist = os.listdir(dr) - print flist - """ add a list of all files in the tagdirectory - """ - res = ['

Files created by makeTagDirectory

\n'] - - flist.sort() - for i,f in enumerate(flist): - if not(os.path.isdir(f)): - fn = os.path.split(f)[-1] - res.append('\n' % (fn,getFileString(fn, dr))) - - res.append('
%s
\n') - - return res - -if __name__ == '__main__': - op = optparse.OptionParser() - op.add_option('-e', '--executable', default='makeTagDirectory') - op.add_option('-o', '--htmloutput', default=None) - op.add_option('-f', '--format', default="sam") - opts, args = op.parse_args() - #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable - - #if not os.path.exists(opts.outputdir): - #os.makedirs(opts.outputdir) - f = makeTagDirectory(opts, args) - - html,retval = f.run_makeTagDirectory() - f = open(opts.htmloutput, 'w') - f.write(''.join(html)) - f.close() - if retval <> 0: - print >> sys.stderr, serr # indicate failure - - - diff -r 0bc4439da640 -r d27851e0cbbd makeTagDirectory.xml --- a/makeTagDirectory.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ - - - homer - - Simple wrapper for makeTagDirectory. Used by findPeaks - - makeTagDirectory.py ${tagDir.files_path} - #for $alignF in $alignmentFiles - $alignF.file -f $alignF.file.ext - #end for - -o $tagDir - 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer makeTagDirectory** - - For more options, look under: "Command line options" - - http://biowhat.ucsd.edu/homer/ngs/tagDir.html - -**Parameter list** - -Command line options (not all of them are supported):: - - Usage: makeTagDirectory <directory> <alignment file 1> [file 2] ... [options] - - Creates a platform-independent 'tag directory' for later analysis. - Currently BED, eland, bowtie, and sam files are accepted. The program will try to - automatically detect the alignment format if not specified. Program will also - unzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly - Existing tag directories can be added or combined to make a new one using -d/-t - If more than one format is needed and the program cannot auto-detect it properly, - make separate tag directories by running the program separately, then combine them. - To perform QC/manipulations on an existing tag directory, add "-update" - - Options: - -fragLength <# | given> (Set estimated fragment length - given: use read lengths) - By default treats the sample as a single read ChIP-Seq experiment - -format <X> where X can be: (with column specifications underneath) - bed - BED format files: - (1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-) - -force5th (5th column of BED file contains # of reads mapping to position) - sam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM) - -unique (keep if there is a single best alignment based on mapq) - -mapq <#> (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:) - -keepOne (keep one of the best alignments even if others exist) - -keepAll (include all alignments in SAM file) - -mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag) - bowtie - output from bowtie (run with --best -k 2 options) - (1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo) - eland_result - output from basic eland - (1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr, - 8:position,9:F/R,10-:mismatches - eland_export - output from illumina pipeline (22 columns total) - (1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand) - eland_extended - output from illumina pipeline (4 columns total) - (1:read name,2:sequence,3:match stats,4:positions[,]) - mCpGbed - encode style mCpG reporting in extended BED format, no auto-detect - (1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC) - allC - Lister style output files detailing the read information about all cytosines - (1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C - -minCounts <#> (minimum number of reads to report mC/C ratios, default: 10) - -mCcontext <CG|CHG|CHH|all> (only use C's in this context, default: CG) - HiCsummary - minimal paired-end read mapping information - (1:readname,2:chr1,3:5'pos1,4:strand1,5:chr2,6:5'pos2,7:strand2) - -force5th (5th column of BED file contains # of reads mapping to position) - -d <tag directory> [tag directory 2] ... (add Tag directory to new tag directory) - -t <tag file> [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory) - -single (Create a single tags.tsv file for all "chromosomes" - i.e. if >100 chromosomes) - -update (Use current tag directory for QC/processing, do not parse new alignment files) - -tbp <#> (Maximum tags per bp, default: no maximum) - -precision <1|2|3> (number of decimal places to use for tag totals, default: 1) - - GC-bias options: - -genome <genome version> (To see available genomes, use "-genome list") - -or- (for custom genomes): - -genome <path-to-FASTA file or directory of FASTA files> - - -checkGC (check Sequence bias, requires "-genome") - -freqStart <#> (offset to start calculating frequency, default: -50) - -freqEnd <#> (distance past fragment length to calculate frequency, default: +50) - -oligoStart <#> (oligo bias start) - -oligoEnd <#> (oligo bias end) - -normGC <target GC profile file> (i.e. tagGCcontent.txt file from control experiment) - Use "-normGC default" to match the genomic GC distribution - -normFixedOligo <oligoFreqFile> (normalize 5' end bias, "-normFixedOligo default" ok) - -minNormRatio <#> (Minimum deflation ratio of tag counts, default: 0.25) - -maxNormRatio <#> (Maximum inflation ratio of tag counts, default: 2.0) - -iterNorm <#> (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the - resulting distrubtion is no more than #% different than target, i.e. 0.1,default: off) - - Paired-end/HiC options - -illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1) - -removePEbg (remove paired end tags within 1.5x fragment length on same chr) - -PEbgLength <#> (remove PE reads facing on another within this distance, default: 1.5x fragLen) - -restrictionSite <seq> (i.e. AAGCTT for HindIII, assign data < 1.5x fragment length to sites) - Must specify genome sequence directory too. (-rsmis <#> to specify mismatches, def: 0) - -both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all) - -removeSelfLigation (removes reads linking same restriction fragment) - -removeRestrictionEnds (removes reads starting on a restriction fragment) - -assignMidPoint (will place reads in the middle of HindIII fragments) - -restrictionSiteLength <#> (maximum distance from restriction site, default: 1.5x fragLen) - -removeSpikes <size bp> <#> (remove tags from regions with > than # times - the average tags per size bp, suggest "-removeSpikes 10000 5") - - - - - diff -r 0bc4439da640 -r d27851e0cbbd pos2bed.xml --- a/pos2bed.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - homer - - - - - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - Converts: homer peak positions -(to)-> BED format - - **Homer pos2bed.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 0bc4439da640 -r d27851e0cbbd tool_dependencies.xml --- a/tool_dependencies.xml Thu Dec 20 18:25:21 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - - - - - - http://biowhat.ucsd.edu/homer/configureHomer.pl - perl ./configureHomer.pl -install - - - ./ - $INSTALL_DIR - - - $INSTALL_DIR/bin - - - - - I'm sorry but this does not work - - - - -