1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fbbaafe86af3/ changeset: r5514:fbbaafe86af3 user: fubar date: 2011-05-08 21:59:28 summary: fix history reference parameter name in gcbias and index reference in ASmetrics affected #: 2 files (46 bytes) --- a/tools/picard/rgPicardASMetrics.xml Sun May 08 08:47:53 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Sun May 08 15:59:28 2011 -0400 @@ -5,9 +5,8 @@ --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": - --ref "$genomeSource.ownFile" -#end if -#if $genomeSource.refGenomeSource == "indexed": + --ref-file "$genomeSource.ownFile" +#else --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" #end if </command> --- a/tools/picard/rgPicardGCBiasMetrics.xml Sun May 08 08:47:53 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Sun May 08 15:59:28 2011 -0400 @@ -5,7 +5,7 @@ --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar -x "$maxheap" #if $genomeSource.refGenomeSource == "history": - --own_ref "$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] }" #end if Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.