diff SMART/galaxy/getWigData.xml @ 31:0ab839023fe4

Uploaded

--- a/SMART/galaxy/getWigData.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/getWigData.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,28 +1,17 @@
-<tool id="getWigData" name="get WIG data">
+<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="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="tagName" type="text" value="None" label="tag option (compulsory 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"/>       
+        <data format="gff3" name="outputFile" label="[getWigData -> gff3] 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>