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1 <tool id="getWigDistance" name="get WIG distance">
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6
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2 <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6
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6 <command interpreter="python">
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7 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile
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8 </command>
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9
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10 <inputs>
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11 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
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12 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
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13 <param name="distance" type="integer" value="1000" label="Distance around positions."/>
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14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>
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6
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15 </inputs>
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16
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17 <outputs>
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18 <data name="outputFile" format="png" label="[get WIG distance] PNG output file"/>
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19 </outputs>
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20
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21 <help>
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22 Plots the average data contained in a set of WIG files (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) around the first nucleotides of a annotation file.
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23
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24 The tool needs an transcript list, some WIG files, and a distance. For each transcript, it collects all the values around its first nucleotide, the radius being given by the distance. Then, it computes the average value for each position. A point (*x*, *y*) means that the average value in the WIG file for a nucleotide distant by *x* nucleotides from the first nucleotide of an input transcript is *y*.
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25
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26 You can possibly use a log scale for the *y*-axis.
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27 </help>
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28 </tool>
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