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comparison SMART/galaxy/getWigDistance.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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30:5677346472b5 31:0ab839023fe4
1 <tool id="getWigDistance" name="get WIG distance"> 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> 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"> 3 <command interpreter="python">
7 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile 4 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile
8 </command> 5 </command>
9 6
10 <inputs> 7 <inputs>
11 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> 8 <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/>
12 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> 9 <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/>
13 <param name="distance" type="integer" value="1000" label="Distance around positions."/> 10 <param name="distance" type="integer" value="1000" label="distance option (compulsory option)" help="Distance around position.Be Careful! The value must be upper than 0"/>
14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/> 11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>
15 </inputs> 12 </inputs>
16 13
17 <outputs> 14 <outputs>
18 <data name="outputFile" format="png" label="[get WIG distance] PNG output file"/> 15 <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/>
19 </outputs> 16 </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> 17 </tool>