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Daniel Blankenberg committed 49c4823

Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.

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tools/picard/rgPicardGCBiasMetrics.xml

     --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>