Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getWigDistance.xml @ 38:2c0c0a89fad7
Uploaded
author | m-zytnicki |
---|---|
date | Thu, 02 May 2013 09:56:47 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
37:d22fadc825e3 | 38:2c0c0a89fad7 |
---|---|
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 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile | |
8 </command> | |
9 | |
10 <inputs> | |
11 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> | |
12 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> | |
13 <param name="distance" type="integer" value="1000" label="Distance around positions."/> | |
14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/> | |
15 </inputs> | |
16 | |
17 <outputs> | |
18 <data name="outputFile" format="png" label="[get WIG distance] PNG output file"/> | |
19 </outputs> | |
20 | |
21 <help> | |
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. | |
23 | |
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*. | |
25 | |
26 You can possibly use a log scale for the *y*-axis. | |
27 </help> | |
28 </tool> |