From 213986aa7fad8ca594a80495ce07c19e40fda026 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 18 Apr 2014 12:34:08 -0400
Subject: [PATCH] Update MAF to interval to use job working directory instead
 of __new_file_path__.

---
 tools/maf/maf_to_interval.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/maf/maf_to_interval.xml b/tools/maf/maf_to_interval.xml
index 22362fa50fa..d127a6f0813 100644
--- a/tools/maf/maf_to_interval.xml
+++ b/tools/maf/maf_to_interval.xml
@@ -1,6 +1,6 @@
 <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True">
   <description>Converts a MAF formatted file to the Interval format</description>
-  <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command>
+  <command interpreter="python">maf_to_interval.py "${ input1 }" "${ out_file1 }" "${ out_file1.id }" "." "${ input1.dbkey }" "${ species }" "${ input1.metadata.species }" "${ complete_blocks }" "${ remove_gaps }"</command>
   <inputs>
     <param format="maf" name="input1" type="data" label="MAF file to convert"/>
     <param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species.">