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18
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1 <tool id="getWigData" name="get WIG data">
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6
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2 <description>Compute the average data for some genomic coordinates using WIG files</description>
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18
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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/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
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8 </command>
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9
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10 <inputs>
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15
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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="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/>
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6
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14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>
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15 </inputs>
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16
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17 <outputs>
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18 <data format="gff3" name="outputFile" label="[get WIG data] output file"/>
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6
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19 </outputs>
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15
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20
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21 <help>
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22 Reads a transcript list, computes the average value of some WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) for each transcript and adds a tag corresponding to this average value to the transcript.
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23
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24 The script finds all the data which correspond to the genomic coordinates of a transcript, average these data and store the result into a tag. Then, the transcripts are written in an output file, together with the tag.
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25
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26 You can then plot your data using *plotTranscriptList.py*.
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27 </help>
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6
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28 </tool>
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