Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getWigDistance.xml @ 15:440ceca58672
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:08:07 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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14:c79b9ae3f65f | 15:440ceca58672 |
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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> |