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