Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/getWigDistance.xml @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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--- a/SMART/galaxy/getWigDistance.xml Mon Apr 29 03:45:52 2013 -0400 +++ b/SMART/galaxy/getWigDistance.xml Tue Apr 30 14:33:21 2013 -0400 @@ -1,28 +1,17 @@ -<tool id="getWigDistance" name="get WIG distance"> +<tool id="getWigDistance" name="get wig distance"> <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description> - <requirements> - <requirement type="set_environment">PYTHONPATH</requirement> - </requirements> <command interpreter="python"> ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile </command> <inputs> - <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> - <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> - <param name="distance" type="integer" value="1000" label="Distance around positions."/> - <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/> + <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/> + <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/> + <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"/> + <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/> </inputs> <outputs> - <data name="outputFile" format="png" label="[get WIG distance] PNG output file"/> + <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/> </outputs> - - <help> -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. - -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*. - -You can possibly use a log scale for the *y*-axis. - </help> </tool>