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view findPeaks.xml @ 24:b3b65304ee72 draft
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author | kevyin |
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date | Thu, 20 Dec 2012 17:52:56 -0500 |
parents | 687df269e597 |
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<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>