1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d2032d37013f/ changeset: r5476:d2032d37013f user: fubar date: 2011-04-28 22:25:09 summary: fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias affected #: 3 files (41 bytes) --- a/tools/picard/picard_ReorderSam.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Thu Apr 28 16:25:09 2011 -0400 @@ -121,7 +121,7 @@ **Picard documentation** -This is a Galaxy interface for Picard-tool_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. +This is a Galaxy interface for Picard-tools_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 16:25:09 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 ), $__app__.tool_data_tables[ 'srma_index' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" #end if </command> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="srma_index"> + <options from_data_table="srma_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options> --- a/tools/rgenetics/rgfakePhe.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/rgenetics/rgfakePhe.xml Thu Apr 28 16:25:09 2011 -0400 @@ -1,6 +1,5 @@ <tool id="fakePhe1" name="Null phenotypes"><description>for testing</description> - <code file="rgfakePhe_code.py"/><command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' "$title1" '$ppheout' '$ppheout.files_path' '$script_file' </command> 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.