Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/getWigDistance.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/getWigDistance.xml Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,28 @@ +<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."/> + </inputs> + + <outputs> + <data name="outputFile" format="png" label="[get WIG distance] 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>