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comparison findPeaks.xml @ 20:90db049d8f68 draft

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author kevyin
date Wed, 19 Dec 2012 20:20:00 -0500
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19:251442d07ef8 20:90db049d8f68
1 <tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2">
2 <requirements>
3 <requirement type="package" version="4.1">homer</requirement>
4 </requirements>
5 <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description>
6 <!--<version_command></version_command>-->
7 <command>
8 findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
9
10 #if $control_tagDir:
11 -i $control_tagDir.extra_files_path
12 #end if
13
14 2&gt; $out_log || echo "Error running findPeaks." >&amp;2
15 </command>
16 <inputs>
17 <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" />
18 <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" />
19 <param type="text" name="options" label="Extra options" value="" help="See link below for more options">
20 <sanitizer>
21 <valid initial="string.printable">
22 <remove value="&apos;"/>
23 <remove value="/"/>
24 </valid>
25 <mapping initial="none">
26 <add source="&apos;" target="__sq__"/>
27 </mapping>
28 </sanitizer>
29 </param>
30 </inputs>
31 <outputs>
32 <!--<data format="html" name="html_outfile" label="index" />-->
33 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
34 <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
35 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
36 </outputs>
37 <tests>
38 <test>
39 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
40 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
41 </test>
42 </tests>
43
44 <help>
45
46 .. class:: infomark
47
48 **Homer findPeaks**
49
50 For more options, look under: "Command line options for findPeaks"
51
52 http://biowhat.ucsd.edu/homer/ngs/peaks.html
53
54 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
55
56 **Parameter list**
57
58 Command line options (not all of them are supported)::
59
60 Usage: findPeaks &lt;tag directory&gt; [options]
61
62 Finds peaks in the provided tag directory. By default, peak list printed to stdout
63
64 General analysis options:
65 -o &lt;filename|auto&gt; (file name for to output peaks, default: stdout)
66 &quot;-o auto&quot; will send output to &quot;&lt;tag directory&gt;/peaks.txt&quot;, &quot;.../regions.txt&quot;,
67 or &quot;.../transcripts.txt&quot; depending on the &quot;-style&quot; option
68 -style &lt;option&gt; (Specialized options for specific analysis strategies)
69 factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt, default)
70 histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt)
71 groseq (de novo transcript identification from GroSeq data, transcripts.txt)
72 tss (TSS identification from 5&apos; RNA sequencing, tss.txt)
73 dnase (Hypersensitivity [crawford style (nicking)], peaks.txt)
74
75 chipseq/histone options:
76 -i &lt;input tag directory&gt; (Experiment to use as IgG/Input/Control)
77 -size &lt;#&gt; (Peak size, default: auto)
78 -minDist &lt;#&gt; (minimum distance between peaks, default: peak size x2)
79 -gsize &lt;#&gt; (Set effective mappable genome size, default: 2e9)
80 -fragLength &lt;#|auto&gt; (Approximate fragment length, default: auto)
81 -inputFragLength &lt;#|auto&gt; (Approximate fragment length of input tags, default: auto)
82 -tbp &lt;#&gt; (Maximum tags per bp to count, 0 = no limit, default: auto)
83 -inputtbp &lt;#&gt; (Maximum tags per bp to count in input, 0 = no limit, default: auto)
84 -strand &lt;both|separate&gt; (find peaks using tags on both strands or separate, default:both)
85 -norm # (Tag count to normalize to, default 10000000)
86 -region (extends start/stop coordinates to cover full region considered &quot;enriched&quot;)
87 -center (Centers peaks on maximum tag overlap and calculates focus ratios)
88 -nfr (Centers peaks on most likely nucleosome free region [works best with mnase data])
89 (-center and -nfr can be performed later with &quot;getPeakTags&quot;
90
91 Peak Filtering options: (set -F/-L/-C to 0 to skip)
92 -F &lt;#&gt; (fold enrichment over input tag count, default: 4.0)
93 -P &lt;#&gt; (poisson p-value threshold relative to input tag count, default: 0.0001)
94 -L &lt;#&gt; (fold enrichment over local tag count, default: 4.0)
95 -LP &lt;#&gt; (poisson p-value threshold relative to local tag count, default: 0.0001)
96 -C &lt;#&gt; (fold enrichment limit of expected unique tag positions, default: 2.0)
97 -localSize &lt;#&gt; (region to check for local tag enrichment, default: 10000)
98 -inputSize &lt;#&gt; (Size of region to search for control tags, default: 2x peak size)
99 -fdr &lt;#&gt; (False discovery rate, default = 0.001)
100 -poisson &lt;#&gt; (Set poisson p-value cutoff, default: uses fdr)
101 -tagThreshold &lt;#&gt; (Set # of tags to define a peak, default: 25)
102 -ntagThreshold &lt;#&gt; (Set # of normalized tags to define a peak, by default uses 1e7 for norm)
103 -minTagThreshold &lt;#&gt; (Absolute minimum tags per peak, default: expected tags per peak)
104
105 GroSeq Options: (Need to specify &quot;-style groseq&quot;):
106 -tssSize &lt;#&gt; (size of region for initiation detection/artifact size, default: 250)
107 -minBodySize &lt;#&gt; (size of regoin for transcript body detection, default: 1000)
108 -maxBodySize &lt;#&gt; (size of regoin for transcript body detection, default: 10000)
109 -tssFold &lt;#&gt; (fold enrichment for new initiation dectection, default: 4.0)
110 -bodyFold &lt;#&gt; (fold enrichment for new transcript dectection, default: 4.0)
111 -endFold &lt;#&gt; (end transcript when levels are this much less than the start, default: 10.0)
112 -fragLength &lt;#&gt; (Approximate fragment length, default: 150)
113 -uniqmap &lt;directory&gt; (directory of binary files specifying uniquely mappable locations)
114 Download from http://biowhat.ucsd.edu/homer/groseq/
115 -confPvalue &lt;#&gt; (confidence p-value: 1.00e-05)
116 -minReadDepth &lt;#&gt; (Minimum initial read depth for transcripts, default: auto)
117 -pseudoCount &lt;#&gt; (Pseudo tag count, default: 2.0)
118 -gtf &lt;filename&gt; (Output de novo transcripts in GTF format)
119 &quot;-o auto&quot; will produce &lt;dir&gt;/transcripts.txt and &lt;dir&gt;/transcripts.gtf
120 </help>
121 </tool>
122