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README annotatePeaks.xml bed2pos.xml findPeaks.xml makeTagDirectory.py makeTagDirectory.xml pos2bed.xml tool_dependencies-disabled.xml |
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diff -r a6d9f6e5840f -r 71e1c2e46752 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,15 @@ +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 + |
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diff -r a6d9f6e5840f -r 71e1c2e46752 annotatePeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotatePeaks.xml Wed Dec 19 20:21:06 2012 -0500 |
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b'@@ -0,0 +1,164 @@\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 a6d9f6e5840f -r 71e1c2e46752 bed2pos.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed2pos.xml Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,37 @@ +<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 a6d9f6e5840f -r 71e1c2e46752 findPeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findPeaks.xml Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,122 @@ +<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 a6d9f6e5840f -r 71e1c2e46752 makeTagDirectory.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/makeTagDirectory.py Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,94 @@ +""" + + +""" +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 a6d9f6e5840f -r 71e1c2e46752 makeTagDirectory.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/makeTagDirectory.xml Wed Dec 19 20:21:06 2012 -0500 |
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b'@@ -0,0 +1,146 @@\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 a6d9f6e5840f -r 71e1c2e46752 pos2bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pos2bed.xml Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,37 @@ +<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($input_peak.name))[0]#.log" /> + </outputs> + <tests> + <test> + <!--<param name="input_file" value="extract_genomic_dna.fa" />--> + <!--<output name="html_file" file="sample_output.html" ftype="html" />--> + </test> + </tests> + + <help> + .. class:: infomark + + Converts: homer peak positions -(to)-> BED format + + **Homer pos2bed.pl** + + http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html + </help> +</tool> + |
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diff -r a6d9f6e5840f -r 71e1c2e46752 tool_dependencies-disabled.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies-disabled.xml Wed Dec 19 20:21:06 2012 -0500 |
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@@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="homer" version="4.1"> + <install version="4.1"> + <actions> + <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action> + <!--<action type="shell_command">perl ./configureHomer.pl -install</action>--> + <!--<action type="shell_command">perl ./configureHomer.pl -install hg19</action>--> + <action type="move_directory_files"> + <source_directory>./</source_directory> + <destination_directory>$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> + I'm sorry but this does not work + + </readme> + </package> +</tool_dependency> + |