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1 <tool id="bigWigSummary" name="bigWigSummary">
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2 <description> Extract summary information from a bigWig file. </description>
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3 <command>
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4 bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="bigwig" label="Input"/>
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8 <param name="chrom" type="text" value="chr" label="Chromosome" help="E.g. 'chr7'"/>
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9 <param name="start" type="integer" value="" label="Start coordinate" help="BED format (0-based)."/>
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10 <param name="end" type="integer" value="" label="End coordinate" help="BED format (0-based)."/>
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11 <param name="dataPoints" type="integer" value="1" label="Number of (equal) parts to break down the selected region." help="Choose 1 for simple summary."/>
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12 <param name="type" type="select" label="Operation">
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13 <option value="mean">Average value in region (default)</option>
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14 <option value="min">Minimum value in region</option>
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15 <option value="max">Maximum value in region</option>
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16 <option value="std">Standard deviation in region</option>
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17 <option value="coverage">Percentage of region that is covered</option>
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18 </param>
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19 </inputs>
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20
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21 <outputs>
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22 <data format="text" name="output"/>
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23 </outputs>
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24
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25 <tests>
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26 <test>
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27 <param name="input" value="1.bigwig" />
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28 <param name="chrom" value="chr21" />
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29 <param name="start" value="10000000" />
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30 <param name="end" value="50000000" />
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31 <param name="dataPoints" value="3" />
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32 <param name="type" value="std" />
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22
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33 <output name="output" file="1.txt" />
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34 </test>
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35 </tests>
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36 <help>
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37
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38 **Usage**
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39 * bigWigSummary file.bigWig chrom start end dataPoints
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40 * Get summary data from bigWig for indicated region, broken into dataPoints equal parts. (Use dataPoints=1 for simple summary.)
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41
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42 </help>
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43 </tool>
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