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

Uploaded

--- a/SMART/galaxy/modifyGenomicCoordinates.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/modifyGenomicCoordinates.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
   <description>Extend or shrink a list of genomic coordinates.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
   <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
 			-f bed
@@ -118,15 +121,15 @@
   </inputs>
 
   <outputs>
-    <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/>
+    <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
   </outputs>
 
   <help>
 This tool reads a list of transcripts and modifies each feature by:
 
-- shrinking it to the $ n $ first nucleotides or the *n* last nucleotides, or
+- shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
 
-- extending it to $ n $ nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
+- extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
 
 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).