# HG changeset patch
# User m-zytnicki
# Date 1392021549 18000
# Node ID 2a4884ba3e5cda00462a038499f77aff61aa1b5d
# Parent  5f5c9b74c2dd26aa9ffeef5687aa168212ceb575
Uploaded

diff -r 5f5c9b74c2dd -r 2a4884ba3e5c SMART/galaxy/removeExonLines.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/removeExonLines.xml	Mon Feb 10 03:39:09 2014 -0500
@@ -0,0 +1,18 @@
+<tool id="removeExonLines" name="remove exon lines">
+  <description>Removes the introns of the transcript files.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+  <command interpreter="python"> ../Java/Python/RemoveExons.py -i $inputFile -f gff3 -o $outputFile  </command>
+  <inputs>
+		<param name="inputFile" format="gff3" type="data" label="Input File"/>
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[remove introns] output file"/>
+  </outputs>
+
+  <help>
+	Simply remove the introns of the input file, thus getting the unmatured transcript.
+  </help>
+</tool>
diff -r 5f5c9b74c2dd -r 2a4884ba3e5c SMART/galaxy/removeIntrons.xml
--- a/SMART/galaxy/removeIntrons.xml	Fri Feb 07 11:53:36 2014 -0500
+++ b/SMART/galaxy/removeIntrons.xml	Mon Feb 10 03:39:09 2014 -0500
@@ -15,22 +15,22 @@
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
-				<param name="inputFileName" format="bed" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="bed" type="data" label="Input File"/>
 			</when>
 			<when value="gff">
-				<param name="inputFileName" format="gff" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="gff" type="data" label="Input File"/>
 			</when>
 			<when value="gff2">
-				<param name="inputFileName" format="gff2" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
 			</when>
 			<when value="gff3">
-				<param name="inputFileName" format="gff3" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
 			</when>
 			<when value="sam">
-				<param name="inputFileName" format="sam" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="sam" type="data" label="Input File"/>
 			</when>
 			<when value="gtf">
-				<param name="inputFileName" format="gtf" type="data" label="Input File 1"/>
+				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
 			</when>
 		</conditional>
   </inputs>