diff SMART/galaxy/plotCoverage.xml @ 18:94ab73e8a190

Uploaded

--- a/SMART/galaxy/plotCoverage.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/plotCoverage.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
 <tool id="plotCoverage" name="plot coverage">
 	<description>Plot the coverage of the first data with respect to the second one.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
 	<command interpreter="python">
 		../Java/Python/WrappPlotCoverage.py -i $formatType.inputFileName1
 		#if $formatType.FormatInputFileName1 == 'bed':
@@ -106,8 +109,8 @@
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
-				<option value="gff2">sam</option>
-				<option value="gff3">gtf</option>
+				<option value="sam">sam</option>
+				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
 				<param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
@@ -256,7 +259,7 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
+		<data name="outputFile" format="tar" label="[plot coverage] tar output file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
 	</outputs> 
 	
     <help>
@@ -264,7 +267,7 @@
 
 Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements).
 
-The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) $ means that *y* reads cover the *x*th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense).
+The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) means that *y* reads cover the *x* th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense).
 
 This script gives a .tar out file, if you want to take look at the results, you have to download it.
     </help>