--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/modifyGenomicCoordinates.xml	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,135 @@
+<tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
+  <description>Extend or shrink a list of genomic coordinates.</description>
+  <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.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
+		#elif $formatType.FormatInputFileName == 'sam':
+			-f sam
+		#elif $formatType.FormatInputFileName == 'gtf':
+			-f gtf
+		#end if
+		
+  		#if $OptionStart.start == "Yes":
+			-s $OptionStart.startValue
+  		#end if
+  	
+  		#if $OptionEnd.end == "Yes":
+			-e $OptionEnd.endValue
+  		#end if
+  		
+  		#if $OptionFivePrim.five == "Yes":
+			-5 $OptionFivePrim.fivePValue
+  		#end if
+  	
+  		#if $OptionTroisP.TroisP == "Yes":
+			-3 $OptionTroisP.ThreePValue
+  		#end if
+  		
+  		-o $outputFile  
+  </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>
+				<option value="sam">sam</option>
+				<option value="gtf">gtf</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>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
+			</when>
+		</conditional>
+  
+		<conditional name="OptionStart">
+			<param name="start" type="select" label="shrink to the start of the feature">
+				<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="shrink to the end of the feature">
+				<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>    
+
+		
+		<conditional name="OptionFivePrim">
+			<param name="five" type="select" label="extend to the 5' direction">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="fivePValue" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>  
+		
+		<conditional name="OptionTroisP">
+			<param name="TroisP" type="select" label="extend to the 3' direction">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="ThreePValue" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		
+		 
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] 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
+
+- 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!).
+
+The tool needs a transcript file, its format, and outputs a new transcript file.
+  </help>
+</tool>