diff SMART/galaxy/getWigDistance.xml @ 38:2c0c0a89fad7

Uploaded

--- /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>