1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c6f70cccce28/ changeset: c6f70cccce28 user: dan date: 2011-11-30 19:29:21 summary: Add no_options validator to built-in reference genome selector in GATK tools. affected #: 13 files diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -146,6 +146,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -194,6 +194,7 @@ <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> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -124,6 +124,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -112,6 +112,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -129,6 +129,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -154,6 +154,7 @@ <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> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -157,6 +157,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -109,6 +109,7 @@ <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -121,6 +121,7 @@ <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -160,6 +160,7 @@ <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -110,6 +110,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -156,6 +156,7 @@ <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -96,6 +96,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"><!-- FIX ME!!!! 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