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comparison metaintv.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="metaintv" name="binned-average">
2 <description>from bigwig</description>
3 <command interpreter="python">binnedAverage.py $bwfile $intvfile $nbin $outfile $outplot </command>
4 <inputs>
5 <param name="intvfile" format="bed" type="data" label="BED file (require strand in column 6)"/>
6 <param name="bwfile" format="bigwig" type="data" label="BigWig file"/>
7 <param name="nbin" type="integer" value="20" label="number of bins"/>
8
9 </inputs>
10 <outputs>
11 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}[data]"/>
12 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
13 </outputs>
14 <help>
15
16 .. class:: infomark
17
18 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 .
19
20 **Example**
21
22 If your original data has the following format:
23
24 +-----+-----+---+------+
25 |chrom|start|end|other2|
26 +-----+-----+---+------+
27
28 and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:
29
30 +-----+-----+---+------+-----+-----+-----+
31 |chrom|start|end|other2|mean1|mean2|mean3|
32 +-----+-----+---+------+-----+-----+-----+
33
34
35 </help>
36 </tool>