|
6
|
1 <tool id="getWigDistance" name="get wig distance">
|
|
|
2 <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $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="distance" type="integer" value="1000" label="Distance around positions."/>
|
|
|
11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>
|
|
6
|
12 </inputs>
|
|
|
13
|
|
|
14 <outputs>
|
|
|
15 <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/>
|
|
|
16 </outputs>
|
|
15
|
17
|
|
|
18 <help>
|
|
|
19 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.
|
|
|
20
|
|
|
21 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*.
|
|
|
22
|
|
|
23 You can possibly use a log scale for the *y*-axis.
|
|
|
24 </help>
|
|
6
|
25 </tool>
|
