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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/getWigData.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,28 @@
+<tool id="getWigData" name="get WIG data">
+    <description>Compute the average data for some genomic coordinates using WIG files</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+    <command interpreter="python">
+		../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$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="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/>
+		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>    
+    </inputs>
+        
+    <outputs>
+        <data format="gff3" name="outputFile" label="[get WIG data] output file"/>       
+    </outputs> 
+
+	<help>
+Reads a transcript list, computes the average value of some WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) for each transcript and adds a tag corresponding to this average value to the transcript.
+
+The script finds all the data which correspond to the genomic coordinates of a transcript, average these data and store the result into a tag. Then, the transcripts are written in an output file, together with the tag.
+
+You can then plot your data using *plotTranscriptList.py*.
+	</help>
+</tool>