From e905e441e37e60f014b73c72e079daecb51a18ce Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 22 Nov 2011 11:56:53 -0500
Subject: [PATCH] Have rgPicardGCBiasMetrics.xml use fields.path approach
 instead of directly filtering on data table.

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

diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml
index 7adce089f04..af3a8b4d420 100644
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -4,9 +4,9 @@
     --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
     -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
- --ref-file "$genomeSource.ownFile"
+ --ref-file "${genomeSource.ownFile}"
 #else:
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ --ref "${genomeSource.index.fields.path}"
 #end if
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>