Mercurial > repos > xuebing > sharplabtool
comparison mytools/metaintv.xml @ 7:f0dc65e7f6c0
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:59:07 -0500 |
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| 6:094f377db4e5 | 7:f0dc65e7f6c0 |
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| 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> |