Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/getWigDistance.xml @ 15:440ceca58672
Uploaded
author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:08:07 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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--- a/SMART/galaxy/getWigDistance.xml Fri Apr 19 10:13:11 2013 -0400 +++ b/SMART/galaxy/getWigDistance.xml Mon Apr 22 11:08:07 2013 -0400 @@ -5,13 +5,21 @@ </command> <inputs> - <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."/> + <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="[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>