From 620e12d364148a0fbe8c60820a3c0a0f7c1561b9 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Thu, 19 Jun 2014 10:41:38 -0400
Subject: working multifasta2otu

---
 src/galaxy/multifasta2otu.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/galaxy/multifasta2otu.xml b/src/galaxy/multifasta2otu.xml
index b80f8b2..eebe246 100644
--- a/src/galaxy/multifasta2otu.xml
+++ b/src/galaxy/multifasta2otu.xml
@@ -1,10 +1,10 @@
 <tool id="multifasta" name="Multifasta">
 	<description>Get Abundances on Multiple Files</description>
-	<command interpreter="bash">multifasta_to_otu -k $kmer -s $db -f &lt;( echo
+	<command>bash -c "multifasta_to_otu -k $kmer -s $db -f &lt;( echo
 #for $input in $inputs:
-"${input}"
+${input}
 #end for
- | xargs -n 1	) -o $output</command>
+ | xargs -n 1	) -o $output"</command>
 	<inputs>
 		<param name="inputs" multiple="true" type="data" format="fasta" label="input fasta"/>
 		<param name="db" type="data" format="data" label="trained database"/>
-- 
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