1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/640ff3d819e5/ changeset: r5481:640ff3d819e5 user: fubar date: 2011-04-29 03:44:35 summary: Finally I think. fasta not .fa for asmetrics and gcbias affected #: 2 files (29 bytes)

--- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:14:46 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:44:35 2011 -0400 @@ -8,7 +8,7 @@ --ref "$genomeSource.ownFile" #end if #if $genomeSource.refGenomeSource == "indexed": - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" #end if </command><requirements><requirement type="package">picard</requirement></requirements> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="srma_indexes"> + <options from_data_table="bwa_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options>

--- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:14:46 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:44:35 2011 -0400 @@ -7,7 +7,7 @@ #if $genomeSource.refGenomeSource == "history": --own_ref "$genomeSource.ownFile" #else: - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" #end if

</command> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="srma_indexes"> + <options from_data_table="bwa_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options> @@ -43,8 +43,8 @@ label="Java heap size. Java is a pig, the art is long but memory is short"><option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option> - <option value="4G">4GB will work for small sized datasets </option> - <option value="8G" >8GB - should generally work...</option> + <option value="4G">4GB for larger datasets </option> + <option value="8G" >8GB use if 4GB fails</option><option value="16G">16GB - try this if 8GB fails</option></param>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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