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comparison SMART/galaxy/getWigDistance.xml @ 15:440ceca58672

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../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
5 </command> 5 </command>
6 6
7 <inputs> 7 <inputs>
8 <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/> 8 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
9 <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/> 9 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
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"/> 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."/> 11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>
12 </inputs> 12 </inputs>
13 13
14 <outputs> 14 <outputs>
15 <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/> 15 <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/>
16 </outputs> 16 </outputs>
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>
17 </tool> 25 </tool>