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README annotatePeaks.xml bed2pos.xml findPeaks.xml makeTagDirectory.py makeTagDirectory.xml pos2bed.xml tool_dependencies.xml |
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| diff -r 687df269e597 -r 686a6b9f3882 README --- a/README Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -Homer wrapper for Galaxy - -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 - |
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| diff -r 687df269e597 -r 686a6b9f3882 annotatePeaks.xml --- a/annotatePeaks.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,164 +0,0 @@\n-<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">\n- <requirements>\n- <requirement type="package" version="4.1">homer</requirement>\n- </requirements>\n- <description></description>\n- <!--<version_command></version_command>-->\n- <command>\n- annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated\n- 2> $out_log || echo "Error running annotatePeaks." >&2\n- </command>\n- <inputs>\n- <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>\n- <param name="genome_selector" type="select" label="Genome version">\n- <option value="hg19" selected="true">hg19</option>\n- </param>\n- <param type="text" name="options" label="Extra options" value="" help="See link below for more options">\n- <sanitizer>\n- <valid initial="string.printable">\n- <remove value="'"/>\n- <remove value="/"/>\n- </valid>\n- <mapping initial="none">\n- <add source="'" target="__sq__"/>\n- </mapping>\n- </sanitizer>\n- </param>\n- </inputs>\n- <outputs>\n- <!--<data format="html" name="html_outfile" label="index" />-->\n- <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->\n- <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />\n- <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />\n- </outputs>\n- <tests>\n- <test>\n- <!--<param name="input_file" value="extract_genomic_dna.fa" />-->\n- <!--<output name="html_file" file="sample_output.html" ftype="html" />-->\n- </test>\n- </tests>\n-\n- <help>\n-\n- .. class:: infomark\n-\n- **Homer annoatePeaks**\n-\n- More information on accepted formats and options\n-\n- http://biowhat.ucsd.edu/homer/ngs/annotation.html\n-\n- TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.\n-\n-**Parameter list**\n-\n-Command line options (not all of them are supported)::\n-\n-\tUsage: annotatePeaks.pl <peak file | tss> <genome version> [additional options...]\n-\n-\tAvailable Genomes (required argument): (name,org,directory,default promoter set)\n-\t\t\t-- or --\n-\t\tCustom: provide the path to genome FASTA files (directory or single file)\n-\n-\tUser defined annotation files (default is UCSC refGene annotation):\n-\t\tannotatePeaks.pl accepts GTF (gene transfer formatted) files to annotate positions relative\n-\t\tto custom annotations, such as those from de novo transcript discovery or Gencode.\n-\t\t-gtf <gtf format file> (-gff and -gff3 can work for those files, but GTF is better)\n-\n-\tPeak vs. tss/tts/rna mode (works with custom GTF file):\n-\t\tIf the first argument is "tss" (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric\n-\t\tanalysis will be carried out. Tag counts and motifs will be found relative to the TSS.\n-\t\t(no position file needed) ["tts" now works too - e.g. 3' end of gene]\n-\t\t["rna" specifies gene bodies, will automaticall set "-size given"]\n-\t\tNOTE: The default TSS peak size is 4000 bp, i.e. +/- 2kb (change with -size option)\n-\t\t-list <gene id list> (subset of genes to perform analysis [unigene, gene id, accession,\n-\t\t\t probe, etc.], default = all promoters)\n-\t\t-cTSS <promoter position file i.e. peak file> (should be centered on TSS)\n-\n-\tPrimary Annotation Options:\n-\t\t-mask (Masked repeats, can also add 'r' to end of genome name)\n-\t\t-m <motif file 1> [motif file 2] ... (list of motifs to find in peaks)\n-\t\t\t-mscore (reports the highest log-odds score within the peak)\n-\t\t\t-nmotifs (reports the number of motifs per peak)\n-\t\t\t-mdist (reports di'..b' analysis to these individuals)\n-\t\t-gene <data file> ... (Adds additional data to result based on the closest gene.\n-\t\t\tThis is useful for adding gene expression data. The file must have a header,\n-\t\t\tand the first column must be a GeneID, Accession number, etc. If the peak\n-\t\t\tcannot be mapped to data in the file then the entry will be left empty.\n-\t\t-go <output directory> (perform GO analysis using genes near peaks)\n-\t\t-genomeOntology <output directory> (perform genomeOntology analysis on peaks)\n-\t\t\t-gsize <#> (Genome size for genomeOntology analysis, default: 2e9)\n-\n-\tAnnotation vs. Histogram mode:\n-\t\t-hist <bin size in bp> (i.e 1, 2, 5, 10, 20, 50, 100 etc.)\n-\t\tThe -hist option can be used to generate histograms of position dependent features relative\n-\t\tto the center of peaks. This is primarily meant to be used with -d and -m options to map\n-\t\tdistribution of motifs and ChIP-Seq tags. For ChIP-Seq peaks for a Transcription factor\n-\t\tyou might want to use the -center option (below) to center peaks on the known motif\n-\t\t** If using "-size given", histogram will be scaled to each region (i.e. 0-100%), with\n-\t\tthe -hist parameter being the number of bins to divide each region into.\n-\t\t\tHistogram Mode specific Options:\n-\t\t\t-nuc (calculated mononucleotide frequencies at each position,\n-\t\t\t\tWill report by default if extracting sequence for other purposes like motifs)\n-\t\t\t-di (calculated dinucleotide frequencies at each position)\n-\t\t\t-histNorm <#> (normalize the total tag count for each region to 1, where <#> is the\n-\t\t\t\tminimum tag total per region - use to avoid tag spikes from low coverage\n-\t\t\t-ghist (outputs profiles for each gene, for peak shape clustering)\n-\t\t\t-rm <#> (remove occurrences of same motif that occur within # bp)\n-\n-\tPeak Centering: (other options are ignored)\n-\t\t-center <motif file> (This will re-center peaks on the specified motif, or remove peak\n-\t\t\tif there is no motif in the peak. ONLY recentering will be performed, and all other\n-\t\t\toptions will be ignored. This will output a new peak file that can then be reanalyzed\n-\t\t\tto reveal fine-grain structure in peaks (It is advised to use -size < 200) with this\n-\t\t\tto keep peaks from moving too far (-mirror flips the position)\n-\t\t-multi (returns genomic positions of all sites instead of just the closest to center)\n-\n-\tAdvanced Options:\n-\t\t-len <#> / -fragLength <#> (Fragment length, default=auto, might want to set to 0 for RNA)\n-\t\t-size <#> (Peak size[from center of peak], default=inferred from peak file)\n-\t\t\t-size #,# (i.e. -size -10,50 count tags from -10 bp to +50 bp from center)\n-\t\t\t-size "given" (count tags etc. using the actual regions - for variable length regions)\n-\t\t-log (output tag counts as log2(x+1+rand) values - for scatter plots)\n-\t\t-sqrt (output tag counts as sqrt(x+rand) values - for scatter plots)\n-\t\t-strand <+|-|both> (Count tags on specific strands relative to peak, default: both)\n-\t\t-pc <#> (maximum number of tags to count per bp, default=0 [no maximum])\n-\t\t-cons (Retrieve conservation information for peaks/sites)\n-\t\t-CpG (Calculate CpG/GC content)\n-\t\t-ratio (process tag values as ratios - i.e. chip-seq, or mCpG/CpG)\n-\t\t-nfr (report nuclesome free region scores instead of tag counts, also -nfrSize <#>)\n-\t\t-norevopp (do not search for motifs on the opposite strand [works with -center too])\n-\t\t-noadj (do not adjust the tag counts based on total tags sequenced)\n-\t\t-norm <#> (normalize tags to this tag count, default=1e7, 0=average tag count in all directories)\n-\t\t-pdist (only report distance to nearest peak using -p, not peak name)\n-\t\t-map <mapping file> (mapping between peak IDs and promoter IDs, overrides closest assignment)\n-\t\t-noann, -nogene (skip genome annotation step, skip TSS annotation)\n-\t\t-homer1/-homer2 (by default, the new version of homer [-homer2] is used for finding motifs)\n-\n-\n- </help>\n-</tool>\n-\n' |
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| diff -r 687df269e597 -r 686a6b9f3882 bed2pos.xml --- a/bed2pos.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.3"> - <requirements> - <requirement type="package" version="4.1">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - </command> - <inputs> - <param format="tabular,bed" name="input_bed" type="data" label="BED file" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - Converts: BED -(to)-> homer peak positions - - **Homer bed2pos.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |
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| diff -r 687df269e597 -r 686a6b9f3882 findPeaks.xml --- a/findPeaks.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,122 +0,0 @@ -<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2"> - <requirements> - <requirement type="package" version="4.1">homer</requirement> - </requirements> - <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description> - <!--<version_command></version_command>--> - <command> - findPeaks $tagDir.extra_files_path $options -o $outputPeakFile - - #if $control_tagDir: - -i $control_tagDir.extra_files_path - #end if - - 2> $out_log || echo "Error running findPeaks." >&2 - </command> - <inputs> - <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" /> - <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" /> - <param type="text" name="options" label="Extra options" value="" help="See link below for more options"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="/"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - - .. 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 - </help> -</tool> - |
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| diff -r 687df269e597 -r 686a6b9f3882 makeTagDirectory.py --- a/makeTagDirectory.py Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 <Output Directory Name> [options] <alignment file1> [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 = ['<div class="module"><h2>Files created by makeTagDirectory</h2><table cellspacing="2" cellpadding="2">\n'] - - flist.sort() - for i,f in enumerate(flist): - if not(os.path.isdir(f)): - fn = os.path.split(f)[-1] - res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, dr))) - - res.append('</table>\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 - - - |
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| diff -r 687df269e597 -r 686a6b9f3882 makeTagDirectory.xml --- a/makeTagDirectory.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,146 +0,0 @@\n-<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">\n- <requirements>\n- <requirement type="package" version="4.1">homer</requirement>\n- </requirements>\n- <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>\n- <!--<version_command></version_command>-->\n- <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} \n- #for $alignF in $alignmentFiles\n- $alignF.file -f $alignF.file.ext\n- #end for\n- -o $tagDir\n- 2> $out_log || echo "Error running homer_makeTagDirectory." >&2\n-\n- </command>\n- <inputs>\n- <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />\n- <param type="text" name="options" label="Extra options" value="" help="See below for more options">\n- <sanitizer>\n- <valid initial="string.printable">\n- <remove value="'"/>\n- <remove value="/"/>\n- </valid>\n- <mapping initial="none">\n- <add source="'" target="__sq__"/>\n- </mapping>\n- </sanitizer>\n- </param>\n- <repeat name="alignmentFiles" title="Alignment Files">\n- <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" />\n- </repeat>\n- </inputs>\n- <outputs>\n- <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->\n- <data format="html" name="tagDir" label="${title} tag directory" />\n- <data format="txt" name="out_log" label="${title}.log" />\n- <!--<data format="html" name="html_outfile" label="index" />-->\n- <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->\n- </outputs>\n-\n-\n- <tests>\n- <!--<test>-->\n- <!--<param name="input_file" value="extract_genomic_dna.fa" />-->\n- <!--<output name="html_file" file="sample_output.html" ftype="html" />-->\n- <!--</test>-->\n- </tests>\n-\n- <help>\n-\n- .. class:: infomark\n-\n- **Homer makeTagDirectory**\n-\n- For more options, look under: "Command line options"\n-\n- http://biowhat.ucsd.edu/homer/ngs/tagDir.html\n-\n-**Parameter list**\n-\n-Command line options (not all of them are supported)::\n-\n-\tUsage: makeTagDirectory <directory> <alignment file 1> [file 2] ... [options]\n-\n-\tCreates a platform-independent 'tag directory' for later analysis.\n-\tCurrently BED, eland, bowtie, and sam files are accepted. The program will try to\n-\tautomatically detect the alignment format if not specified. Program will also\n-\tunzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly\n-\tExisting tag directories can be added or combined to make a new one using -d/-t\n-\tIf more than one format is needed and the program cannot auto-detect it properly,\n-\tmake separate tag directories by running the program separately, then combine them.\n-\tTo perform QC/manipulations on an existing tag directory, add "-update"\n-\n-\tOptions:\n-\t\t-fragLength <# | given> (Set estimated fragment length - given: use read lengths)\n-\t\t\tBy default treats the sample as a single read ChIP-Seq experiment\n-\t\t-format <X> where X can be: (with column specifications underneath)\n-\t\t\tbed - BED format files:\n-\t\t\t\t(1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-)\n-\t\t\t\t-force5th (5th column of BED file contains # of reads mapping to position)\n-\t\t\tsam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM)\n-\t\t\t\t-unique (keep if there is a single best alignment based on mapq)\n-\t\t\t\t\t-mapq <#> (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:)\n-\t\t\t\t-keepOne (keep one of the best alignments even if others exist)\n-\t\t\t\t-keepAll (include all alignments in SAM file)\n-\t\t\t\t-mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag)\n-\t\t\tbowtie - o'..b'st -k 2 options)\n-\t\t\t\t(1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo)\n-\t\t\teland_result - output from basic eland\n-\t\t\t\t(1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr,\n-\t\t\t\t\t\t\t8:position,9:F/R,10-:mismatches\n-\t\t\teland_export - output from illumina pipeline (22 columns total)\n-\t\t\t\t(1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand)\n-\t\t\teland_extended - output from illumina pipeline (4 columns total)\n-\t\t\t\t(1:read name,2:sequence,3:match stats,4:positions[,])\n-\t\t\tmCpGbed - encode style mCpG reporting in extended BED format, no auto-detect\n-\t\t\t\t(1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC)\n-\t\t\tallC - Lister style output files detailing the read information about all cytosines\n-\t\t\t\t(1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C\n-\t\t\t\t-minCounts <#> (minimum number of reads to report mC/C ratios, default: 10)\n-\t\t\t\t-mCcontext <CG|CHG|CHH|all> (only use C's in this context, default: CG)\n-\t\t\tHiCsummary - minimal paired-end read mapping information\n-\t\t\t\t(1:readname,2:chr1,3:5'pos1,4:strand1,5:chr2,6:5'pos2,7:strand2)\n-\t\t-force5th (5th column of BED file contains # of reads mapping to position)\n-\t\t-d <tag directory> [tag directory 2] ... (add Tag directory to new tag directory)\n-\t\t-t <tag file> [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory)\n-\t\t-single (Create a single tags.tsv file for all "chromosomes" - i.e. if >100 chromosomes)\n-\t\t-update (Use current tag directory for QC/processing, do not parse new alignment files)\n-\t\t-tbp <#> (Maximum tags per bp, default: no maximum)\n-\t\t-precision <1|2|3> (number of decimal places to use for tag totals, default: 1)\n-\n-\t\tGC-bias options:\n-\t\t-genome <genome version> (To see available genomes, use "-genome list")\n-\t\t\t-or- (for custom genomes):\n-\t\t-genome <path-to-FASTA file or directory of FASTA files>\n-\n-\t\t-checkGC (check Sequence bias, requires "-genome")\n-\t\t\t-freqStart <#> (offset to start calculating frequency, default: -50)\n-\t\t\t-freqEnd <#> (distance past fragment length to calculate frequency, default: +50)\n-\t\t\t-oligoStart <#> (oligo bias start)\n-\t\t\t-oligoEnd <#> (oligo bias end)\n-\t\t-normGC <target GC profile file> (i.e. tagGCcontent.txt file from control experiment)\n-\t\t\tUse "-normGC default" to match the genomic GC distribution\n-\t\t-normFixedOligo <oligoFreqFile> (normalize 5' end bias, "-normFixedOligo default" ok)\n-\t\t-minNormRatio <#> (Minimum deflation ratio of tag counts, default: 0.25)\n-\t\t-maxNormRatio <#> (Maximum inflation ratio of tag counts, default: 2.0)\n-\t\t-iterNorm <#> (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the\n-\t\t\tresulting distrubtion is no more than #% different than target, i.e. 0.1,default: off)\n-\n-\tPaired-end/HiC options\n-\t\t-illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1)\n-\t\t-removePEbg (remove paired end tags within 1.5x fragment length on same chr)\n-\t\t\t-PEbgLength <#> (remove PE reads facing on another within this distance, default: 1.5x fragLen)\n-\t\t-restrictionSite <seq> (i.e. AAGCTT for HindIII, assign data < 1.5x fragment length to sites)\n-\t\t\tMust specify genome sequence directory too. (-rsmis <#> to specify mismatches, def: 0)\n-\t\t\t-both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all)\n-\t\t\t-removeSelfLigation (removes reads linking same restriction fragment)\n-\t\t\t-removeRestrictionEnds (removes reads starting on a restriction fragment)\n-\t\t\t-assignMidPoint (will place reads in the middle of HindIII fragments)\n-\t\t\t-restrictionSiteLength <#> (maximum distance from restriction site, default: 1.5x fragLen)\n-\t\t-removeSpikes <size bp> <#> (remove tags from regions with > than # times\n-\t\t\tthe average tags per size bp, suggest "-removeSpikes 10000 5")\n-\n-\n- </help>\n-</tool>\n-\n' |
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| diff -r 687df269e597 -r 686a6b9f3882 pos2bed.xml --- a/pos2bed.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,37 +0,0 @@ -<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.3"> - <requirements> - <requirement type="package" version="4.1" >homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - </command> - <inputs> - <param format="tabular" name="input_peak" type="data" label="Homer peak positions" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - Converts: homer peak positions -(to)-> BED format - - **Homer pos2bed.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |
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| diff -r 687df269e597 -r 686a6b9f3882 tool_dependencies.xml --- a/tool_dependencies.xml Wed Dec 19 17:28:55 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,23 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="homer" version="4.1"> - <install version="4.1"> - <actions> - <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action> - <action type="shell_command">perl ./configureHomer.pl -install</action> - <action type="shell_command">perl ./configureHomer.pl -install hg19</action> - <action type="move_directory_files"> - <source_directory>./</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Installs homer - </readme> - </package> -</tool_dependency> - |