Mercurial > repos > xuebing > sharplabtool
comparison bwBinavg.xml @ 11:b7f1d9f8f3bc
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author | xuebing |
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date | Sat, 10 Mar 2012 07:59:27 -0500 |
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10:1558594a3c2e | 11:b7f1d9f8f3bc |
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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> |