From 3cd89ab5a71c13641df1e767fc6932c9d8ef456a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 16 Jan 2008 18:09:37 +0000
Subject: [PATCH] Missed something with MAF tools.

---
 tools/maf/genebed_maf_to_fasta.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/maf/genebed_maf_to_fasta.xml b/tools/maf/genebed_maf_to_fasta.xml
index 5d951a522b8..d42ddd9457e 100644
--- a/tools/maf/genebed_maf_to_fasta.xml
+++ b/tools/maf/genebed_maf_to_fasta.xml
@@ -1,7 +1,7 @@
 <tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks">
   <description>given a set of coding exon intervals</description>
-  <command interpreter="python2.4">#if $maf_source_type.maf_source == "user":#interval_maf_to_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED
-#else:#interval_maf_to_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source  --geneBED
+  <command interpreter="python2.4">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED
+#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source  --geneBED
 #end if
   </command>
   <inputs>