|
6
|
1 <tool id="getWigData" name="get wig data">
|
|
|
2 <description>Compute the average data for some genomic coordinates using WIG files</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
|
|
|
5 </command>
|
|
|
6
|
|
|
7 <inputs>
|
|
15
|
8 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
|
|
|
9 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
|
|
|
10 <param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/>
|
|
6
|
11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>
|
|
|
12 </inputs>
|
|
|
13
|
|
|
14 <outputs>
|
|
|
15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/>
|
|
|
16 </outputs>
|
|
15
|
17
|
|
|
18 <help>
|
|
|
19 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.
|
|
|
20
|
|
|
21 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.
|
|
|
22
|
|
|
23 You can then plot your data using *plotTranscriptList.py*.
|
|
|
24 </help>
|
|
6
|
25 </tool>
|
