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

Uploaded

--- a/SMART/galaxy/changeTagName.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/changeTagName.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,10 +1,9 @@
 <tool id="changeTagName" name="change tag name">
-	<description>Change the name of a tag in a GFF file.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
+	<description>Changes the name of tag of a list of transcripts.</description>
 	<command interpreter="python">
 		../Java/Python/changeTagName.py -i $formatType.inputFileName
+		#if $formatType.FormatInputFileName == 'bed':
+			-f bed
 		#elif $formatType.FormatInputFileName == 'gff':
 			-f gff
 		#elif $formatType.FormatInputFileName == 'gff2':
@@ -22,10 +21,14 @@
 	<inputs>
 		<conditional name="formatType">
 			<param name="FormatInputFileName" type="select" label="Input File Format">
+				<option value="bed">bed</option>
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 			</param>
+			<when value="bed">
+				<param name="inputFileName" format="bed" type="data" label="Input File"/>
+			</when>
 			<when value="gff">
 				<param name="inputFileName" format="gff" type="data" label="Input File"/>
 			</when>
@@ -37,15 +40,15 @@
 			</when>
 		</conditional>
 
-		<param name="Tag" type="text" label="tag option" help="The tag you want to change"/>
-		<param name="name" type="text" label="name option" help="A new name for the tag"/>		
+		<param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
+		<param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/>		
+	
+		
+
 	</inputs>
 
 	<outputs>
-		<data name="outputFileGff" format="gff3" label="[change tag name] Output File"/>
+		<data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/>
 	</outputs> 
 	
-	<help>
-		Change the name of a tag in the 9th field of a GFF3 file (please consult http://www.sequenceontology.org/gff3.shtml to know more about this format).
-	</help>
 </tool>