diff flaimapper-gtf-from-fasta.xml @ 24:bd695d4cb7c4 draft

Uploaded

--- a/flaimapper-gtf-from-fasta.xml	Wed Mar 25 16:19:39 2015 -0400
+++ b/flaimapper-gtf-from-fasta.xml	Sun Mar 29 02:43:11 2015 -0400
@@ -12,11 +12,16 @@
 		gtf-from-fasta
 			 -o $output
 			    $fasta
-			2> stderr.txt ;
-		
-		grep -v '[fai_load] build FASTA index.' stderr.txt >&amp2 ;
 	</command>
 	
+	<stdio>
+		<regex
+			match="[fai_load] build FASTA index." 
+			source="stderr" 
+			level="log" 
+			description="The FASTA file is being indexed." />
+	</stdio>
+	
 	<inputs>
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
 	</inputs>
@@ -25,6 +30,14 @@
 		<data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
 	</outputs>
 	
+	<tests>
+		<test>
+			<param name="fasta" value="ncrnadb09.fa" />
+			
+			<param name="output" value="ncrnadb09.gtf" />
+		</test>
+	</tests>
+	
 	<help>
 FlaiMapper wrapper for Galaxy
 =============================