# HG changeset patch
# User yhoogstrate
# Date 1415373458 18000
# Node ID 83c9552188d1fb736eaa77c8d4d347b6a52e8b98
# Parent  5035af9394d1089a32917a8c7268dc629b564ace
Uploaded

diff -r 5035af9394d1 -r 83c9552188d1 flaimapper.xml
--- a/flaimapper.xml	Fri Nov 07 09:37:14 2014 -0500
+++ b/flaimapper.xml	Fri Nov 07 10:17:38 2014 -0500
@@ -6,6 +6,9 @@
 		<requirement type="package" version="0.7.7">pysam</requirement>
 	</requirements>
 	<command>
+		##rm $mask".tbi"
+		##rm $fasta".fai"
+		
 		flaimapper
 			 -v
 			 -f $output_format
@@ -22,14 +25,14 @@
 		
 		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
 		
-		<param name="output_format" type="select" label="Get">
+		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
+		
+		<param name="output_format" type="select" label="Output format">
 			<option value="1">Tabular (1 fragment per column)</option>
 			<option value="2">Tabular  (1 precursor per column)</option>
 			<option value="3">GenBank</option>
 			<!-- option value="gtf">GTF/GFF</option -->
 		</param>
-		
-		<param name="fasta" type="data" format="fa,fasta" label="Fasta sequence corresponding to reference genome" help="" />
 	</inputs>
 	
 	<outputs>