# HG changeset patch
# User yhoogstrate
# Date 1426847615 14400
# Node ID be98a7b6c94e769e56e536255980374cc1e4dd62
# Parent  71b580f3a3e8e4484fe566042f5f6a518d2504a9
Fixed capturing a non-critical warning that's being send to stderr.

diff -r 71b580f3a3e8 -r be98a7b6c94e flaimapper.xml
--- a/flaimapper.xml	Fri Mar 20 06:04:09 2015 -0400
+++ b/flaimapper.xml	Fri Mar 20 06:33:35 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.2.c">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.2.d">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
 		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
@@ -19,6 +19,12 @@
 		#for $alignment in $alignments
 			$alignment
 		#end for
+		
+		2&gt; stderr.txt ; 
+		
+		grep -v '[fai_load] build FASTA index.' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+		
+		cat stderr.txt >&amp;2
 	</command>
 	
 	<inputs>