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

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Daniel Blankenberg
2011-11-22 11:56:53 -05:00
parent 8e154e55e9
commit e905e441e3
1 changed files with 2 additions and 2 deletions
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tools/picard/rgPicardGCBiasMetrics.xml
+2 -2
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@@ -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>