--- a/flaimapper-gtf-from-fasta.xml	Fri Jul 31 05:30:48 2015 -0400
+++ b/flaimapper-gtf-from-fasta.xml	Fri Jul 31 05:30:55 2015 -0400
@@ -1,43 +1,41 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1">
-	<description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
-	<requirements>
-		<requirement type="package" version="1.2.1">flaimapper</requirement>
-	</requirements>
-	
-	<stdio>
-		<regex
-			match="[fai_load] build FASTA index." 
-			source="stderr" 
-			level="log" 
-			description="The FASTA file is being indexed." />
-	</stdio>
-	
-	<version_command>flaimapper --version</version_command>
-	
-	<command>
-		gtf-from-fasta
-			 -o $output
-			    $fasta
-	</command>
-	
-	<inputs>
-		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
-	</inputs>
-	
-	<outputs>
-		<data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
-	</outputs>
-	
-	<tests>
-		<test>
-			<param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
-			
-			<output name="output" file="test3/reference.gtf" />
-		</test>
-	</tests>
-	
-	<help>
+<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w2">
+    <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
+    <requirements>
+        <requirement type="package" version="1.2.1">flaimapper</requirement>
+    </requirements>
+    
+    <stdio>
+        <regex
+            match="[fai_load] build FASTA index." 
+            source="stderr" 
+            level="log" 
+            description="The FASTA file is being indexed." />
+    </stdio>
+    
+    <version_command>flaimapper --version</version_command>
+    
+    <command><![CDATA[
+        gtf-from-fasta -o $output $fasta
+    ]]></command>
+    
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="This is the FASTA file that fits the used reference genome (e.g. hg19 or a ncRNA database)." />
+    </inputs>
+    
+    <outputs>
+        <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
+            
+            <output name="output" file="test3/reference.gtf" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
 FlaiMapper wrapper for Galaxy
 =============================
 
@@ -100,14 +98,14 @@
 * Repository-Maintainer: Youri Hoogstrate
 * Repository-Developers: Youri Hoogstrate
 
-* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
 
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands).
 
-	</help>
-	
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/btu696</citation>
-	</citations>
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu696</citation>
+    </citations>
 </tool>