1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/520773ea8c87/ changeset: 520773ea8c87 user: dan date: 2011-10-31 14:41:09 summary: GATK tools will now use gatk_picard_indexes data table. affected #: 15 files diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -70,6 +70,11 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/picard_index.loc" /></table> + <!-- Location of Picard dict files valid for GATK --> + <table name="gatk_picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path, tools_valid_for</columns> + <file path="tool-data/picard_index.loc" /> + </table><!-- Location of SRMA dict file and other files --><table name="srma_indexes" comment_char="#"><columns>value, dbkey, name, path</columns> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -11,6 +11,7 @@ -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar" -recalFile "${input_recal}" -outputDir "${output_html.files_path}" + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R" diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -139,10 +139,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -13,6 +13,7 @@ -T "IndelRealigner" -o "${output_bam}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -108,10 +109,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -13,6 +13,7 @@ -T "RealignerTargetCreator" -o "${output_interval}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -104,10 +105,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -13,6 +13,7 @@ -T "TableRecalibration" -o "${output_bam}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -118,10 +119,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -136,11 +136,11 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -146,10 +146,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -102,7 +102,7 @@ <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -114,7 +114,7 @@ </param></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -159,7 +159,7 @@ <param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -106,7 +106,7 @@ <when value="cached"><param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -152,7 +152,7 @@ <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -12,6 +12,7 @@ -T "ValidateVariants" -et "NO_ET" ##ET no phone home + --num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -91,7 +92,7 @@ <when value="cached"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 147f55e7161ceb4ea9fd3d08bd5dedd19fccbec0 -r 520773ea8c879c2ff3705118fa0913673e1c70c6 tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -4,7 +4,7 @@ picard_wrapper.py --input=$inputFile #if $source.indexSource == "built-in" - --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }" + --ref="${source.ref.fields.path}" #else --ref-file=$refFile --species-name=$source.speciesName Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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