comparison bwBinavg.xml @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 <tool id="bwbinavg" name="bigwig summary">
2 <description>for intervals</description>
3 <command interpreter="python">getGenomicScore.py $input $output $score_type $bwfile $nbin $strand $outplot $span</command>
4 <inputs>
5 <param name="input" format="interval" type="data" label="Interval file"/>
6 <param name="bwfile" format="bigwig" type="data" label="BigWig file"/>
7 <param name="score_type" type="select" label="Select score summary type" >
8 <option value="mean" selected="true">mean</option>
9 <option value="max">maximum</option>
10 <option value="min">minimum</option>
11 <option value="std">standard deviation</option>
12 <option value="coverage">coverage:fraction covered</option>
13 </param>
14 <param name="nbin" type="integer" value="1" label="number of bins"/>
15 <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/>
16 <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>
17 </inputs>
18 <outputs>
19 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
20 <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
21 </outputs>
22 <help>
23
24 .. class:: infomark
25
26 Each interval is binned and the average base-resolution score/coverage/density in the bigwig file is added as new columns appended at the end of the original file .
27
28 **Example**
29
30 If your original data has the following format:
31
32 +-----+-----+---+------+
33 |chrom|start|end|other2|
34 +-----+-----+---+------+
35
36 and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:
37
38 +-----+-----+---+------+-----+-----+-----+
39 |chrom|start|end|other2|mean1|mean2|mean3|
40 +-----+-----+---+------+-----+-----+-----+
41
42
43 </help>
44 </tool>