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