1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7bb305f17ba7/ changeset: 7bb305f17ba7 user: dan date: 2012-03-16 16:30:21 summary: Add GATK tools to tool_conf.xml.main. affected #: 1 file diff -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -390,6 +390,39 @@ <tool file="samtools/samtools_flagstat.xml" /><tool file="samtools/samtools_rmdup.xml" /></section> + <section name="NGS: GATK Tools (beta)" id="gatk"> + <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <tool file="gatk/depth_of_coverage.xml" /> + <tool file="gatk/print_reads.xml" /> + + <label text="Realignment" id="gatk_realignment" /> + <tool file="gatk/realigner_target_creator.xml" /> + <tool file="gatk/indel_realigner.xml" /> + + <label text="Base Recalibration" id="gatk_recalibration" /> + <tool file="gatk/count_covariates.xml" /> + <tool file="gatk/table_recalibration.xml" /> + <tool file="gatk/analyze_covariates.xml" /> + + <label text="Genotyping" id="gatk_genotyping" /> + <tool file="gatk/unified_genotyper.xml" /> + + <label text="Annotation" id="gatk_annotation" /> + <tool file="gatk/variant_annotator.xml" /> + + <label text="Filtration" id="gatk_filtration" /> + <tool file="gatk/variant_filtration.xml" /> + <tool file="gatk/variant_select.xml" /> + + <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <tool file="gatk/variant_recalibrator.xml" /> + <tool file="gatk/variant_apply_recalibration.xml" /> + + <label text="Variant Utilities" id="gatk_variant_utilities"/> + <tool file="gatk/variants_validate.xml" /> + <tool file="gatk/variant_eval.xml" /> + <tool file="gatk/variant_combine.xml" /> + </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> 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.