From da3db3020aab7cc5d90a12d5457b04515382f8e4 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 27 Aug 2008 12:06:47 -0400
Subject: [PATCH] Allow the user to optionally set a reference sequence in
 GMAJ.

---
 tools/visualization/GMAJ.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/visualization/GMAJ.xml b/tools/visualization/GMAJ.xml
index 8537e55b4e7..bb9e66e7be4 100644
--- a/tools/visualization/GMAJ.xml
+++ b/tools/visualization/GMAJ.xml
@@ -3,6 +3,7 @@
   <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command>
   <inputs>
       <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
+      <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/>
       <repeat name="annotations" title="Annotations">
         <param name="species" type="select" label="Species of Annotation" multiple="False">
           <options>
@@ -70,7 +71,11 @@
 
 title = "Galaxy: $maf_input.name"
 alignfile = input.maf
+#if $refseq.value:
+refseq = $refseq
+#else:
 refseq = any
+#end if
 tabext = .bed .gff .gtf
 #if $nowarn.value:
 nowarn = $nowarn