diff SMART/galaxy/changeTagName.xml @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/changeTagName.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,54 @@
+<tool id="changeTagName" name="change tag name">
+	<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':
+			-f gff2
+		#elif $formatType.FormatInputFileName == 'gff3':
+			-f gff3
+		#end if
+
+		-t $Tag
+		-n $name
+			
+		-o $outputFileGff 
+	</command>
+
+	<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>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
+			</when>
+		</conditional>
+
+		<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="[changeTagName] Output File"/>
+	</outputs> 
+	
+</tool>