--- a/cuffdiff_wrapper.xml	Tue Oct 01 12:54:00 2013 -0400
+++ b/cuffdiff_wrapper.xml	Wed Oct 09 12:49:03 2013 -0400
@@ -26,14 +26,14 @@
 
             ## Bias correction?
             #if $bias_correction.do_bias_correction == "Yes":
-	        -b
+               -b
                 #if $bias_correction.seq_source.index_source == "history":
-                    --ref_file=$bias_correction.seq_source.ref_file
+                    ## Custom genome from history.
+                    $bias_correction.seq_source.ref_file
                 #else:
-                    --ref_file="None"
+                    ## Built-in genome.
+                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
-                --dbkey=${gtf_input.metadata.dbkey} 
-                --index_dir=${GALAXY_DATA_INDEX_DIR}
             #end if
 
             #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] )
@@ -116,6 +116,7 @@
     </inputs>
 
     <stdio>
+        <regex match="Error" source="both" level="fatal" description="Error"/>
         <regex match=".*" source="both" level="log" description="tool progress"/>
     </stdio>
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Wed Oct 09 12:49:03 2013 -0400
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa