1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/16cf802f9211/ changeset: 16cf802f9211 user: dan date: 2011-11-17 17:13:53 summary: Update GATK to version 1.3. affected #: 19 files diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html --- a/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html +++ b/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html @@ -6,12 +6,29 @@ <p/><ul><li><a href="A Fake phiX Sample.CycleCovariate.dat">A Fake phiX Sample.CycleCovariate.dat</a></li> +<li><a href="A Fake phiX Sample.CycleCovariate.dat.Cycle_hist.pdf">A Fake phiX Sample.CycleCovariate.dat.Cycle_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.CycleCovariate.dat.qual_diff_v_Cycle.pdf">A Fake phiX Sample.CycleCovariate.dat.qual_diff_v_Cycle.pdf</a></li> +<li><a href="A Fake phiX Sample.CycleCovariate.dat.reported_qual_v_Cycle.pdf">A Fake phiX Sample.CycleCovariate.dat.reported_qual_v_Cycle.pdf</a></li><li><a href="A Fake phiX Sample.DinucCovariate.dat">A Fake phiX Sample.DinucCovariate.dat</a></li> +<li><a href="A Fake phiX Sample.DinucCovariate.dat.Dinuc_hist.pdf">A Fake phiX Sample.DinucCovariate.dat.Dinuc_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.DinucCovariate.dat.qual_diff_v_Dinuc.pdf">A Fake phiX Sample.DinucCovariate.dat.qual_diff_v_Dinuc.pdf</a></li> +<li><a href="A Fake phiX Sample.DinucCovariate.dat.reported_qual_v_Dinuc.pdf">A Fake phiX Sample.DinucCovariate.dat.reported_qual_v_Dinuc.pdf</a></li><li><a href="A Fake phiX Sample.HomopolymerCovariate.dat">A Fake phiX Sample.HomopolymerCovariate.dat</a></li> +<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.Homopolymer_hist.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.Homopolymer_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.qual_diff_v_Homopolymer.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.qual_diff_v_Homopolymer.pdf</a></li> +<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.reported_qual_v_Homopolymer.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.reported_qual_v_Homopolymer.pdf</a></li><li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat">A Fake phiX Sample.MinimumNQSCovariate.dat</a></li> +<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.MinimumNQS_hist.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.MinimumNQS_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.qual_diff_v_MinimumNQS.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.qual_diff_v_MinimumNQS.pdf</a></li> +<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.reported_qual_v_MinimumNQS.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.reported_qual_v_MinimumNQS.pdf</a></li><li><a href="A Fake phiX Sample.PositionCovariate.dat">A Fake phiX Sample.PositionCovariate.dat</a></li> +<li><a href="A Fake phiX Sample.PositionCovariate.dat.Position_hist.pdf">A Fake phiX Sample.PositionCovariate.dat.Position_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.PositionCovariate.dat.qual_diff_v_Position.pdf">A Fake phiX Sample.PositionCovariate.dat.qual_diff_v_Position.pdf</a></li> +<li><a href="A Fake phiX Sample.PositionCovariate.dat.reported_qual_v_Position.pdf">A Fake phiX Sample.PositionCovariate.dat.reported_qual_v_Position.pdf</a></li><li><a href="A Fake phiX Sample.QualityScoreCovariate.dat">A Fake phiX Sample.QualityScoreCovariate.dat</a></li> -<li><a href="A.qual_diff_v_Fake.pdf">A.qual_diff_v_Fake.pdf</a></li> +<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_hist.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_hist.pdf</a></li> +<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_v_stated.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_v_stated.pdf</a></li> +<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_rep_hist.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_rep_hist.pdf</a></li></ul></body></html> diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains --- a/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains +++ b/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains @@ -11,4 +11,3 @@ CountCovariatesWalker - Writing raw recalibration data... CountCovariatesWalker - ...done! TraversalEngine - Total runtime -TraversalEngine - 0 reads were filtered out during traversal out of 20 total (0.00%) \ No newline at end of file diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains @@ -10,4 +10,3 @@ UnifiedGenotyper - % confidently called bases of callable loci 100.000 UnifiedGenotyper - Actual calls made 1 TraversalEngine - Total runtime -TraversalEngine - 0 reads were filtered out during traversal out of 20 total (0.00%) diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf @@ -25,4 +25,4 @@ ##contig=<ID=phiX174,length=5386> ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf --- a/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf +++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf @@ -28,4 +28,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf --- a/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf +++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf @@ -30,4 +30,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DB;DP=10;MQ=37.74;MQ0=0;QD=0.00;set=ReferenceInAll GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DP=10;MQ=37.74;MQ0=0;QD=0.00;set=ReferenceInAll GT:DP:PL ./.:10:0,0,0 diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -1,7 +1,7 @@ -<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.3"> +<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.4"><description>- draw plots</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" @@ -13,8 +13,7 @@ -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" + ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough #if $analysis_param_type.analysis_param_type_selector == "advanced": --ignoreQ "${analysis_param_type.ignore_q}" --numRG "${analysis_param_type.num_read_groups}" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -1,7 +1,7 @@ -<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.3"> +<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.4"><description>on BAM files</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -1,7 +1,7 @@ -<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.4"> +<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.5"><description>- perform local realignment</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -1,7 +1,7 @@ -<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.3"> +<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4"><description>for use in local realignment</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -1,7 +1,7 @@ -<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.3"> +<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.4"><description>on BAM files</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -1,7 +1,7 @@ -<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.3"> +<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4"><description>SNP and indel caller</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" @@ -104,7 +104,6 @@ --output_mode "${analysis_param_type.output_mode}" ${analysis_param_type.compute_SLOD} --min_base_quality_score "${analysis_param_type.min_base_quality_score}" - --min_mapping_quality_score "${analysis_param_type.min_mapping_quality_score}" --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}" --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}" --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}" @@ -343,7 +342,6 @@ </param><param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" /><param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" /> - <param name="min_mapping_quality_score" type="integer" value="20" label="Minimum read mapping quality required to consider a read for calling" /><param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1" /><param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" /><param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/> @@ -417,7 +415,6 @@ <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" /><param name="compute_SLOD" /><param name="min_base_quality_score" value="17" /> - <param name="min_mapping_quality_score" value="20" /><param name="max_deletion_fraction" value="-1" /><param name="min_indel_count_for_genotyping" value="2" /><param name="indel_heterozygosity" value="0.000125" /> @@ -471,7 +468,6 @@ standard_min_confidence_threshold_for_emitting The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold) noSLOD If provided, we will not calculate the SLOD min_base_quality_score Minimum base quality required to consider a base for calling - min_mapping_quality_score Minimum read mapping quality required to consider a read for calling max_deletion_fraction Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05] min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run indel_heterozygosity Heterozygosity for indel calling diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.2"> +<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.2"> +<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.2"> +<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.2"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.2"> +<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.3"><description>on VCF files</description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -1,7 +1,7 @@ -<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.2"> +<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" diff -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed -r 16cf802f921189fd5d2a8cba4a04926065afff1c tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -1,7 +1,7 @@ -<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.2"> +<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.3"><description></description><requirements> - <requirement type="package" version="1.2">gatk</requirement> + <requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" 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.