--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/modifyFasta.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,49 @@
+<tool id="modifyFasta" name="modify fasta">
+  <description>Extend or shring a list of sequences.</description>
+  <command interpreter="python"> ../Java/Python/modifyFasta.py -i $inputFile 
+  	#if $OptionStart.start == "Yes":
+			-s $OptionStart.startValue
+  	#end if
+  	
+  	#if $OptionEnd.end == "Yes":
+			-e $OptionEnd.endValue
+  	#end if
+  	-o $outputFile  
+  
+  </command>
+  
+  
+  <inputs>
+    <param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
+	<conditional name="OptionStart">
+			<param name="start" type="select" label="keep first nucleotides">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="startValue" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+	</conditional>
+		
+	<conditional name="OptionEnd">
+			<param name="end" type="select" label="keep last nucleotides">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="endValue" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+	</conditional>   
+  </inputs>
+
+  <outputs>
+    <data format="fasta" name="outputFile" label="[modifyFasta] Output File"/>
+  </outputs>
+
+  <help>
+  </help>
+</tool>