1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8cf1bb73a247/ changeset: 8cf1bb73a247 user: dan date: 2012-02-23 19:48:09 summary: Correct typo in GATK EvalVariant tool. affected #: 3 files
diff -r 981e31193e25dc5db1923ef2d77c88b99347d670 -r 8cf1bb73a24748aea056a0f1e218783dcaac6e1b test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report --- /dev/null +++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report @@ -0,0 +1,30 @@ +##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites +CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate +CompOverlap dbsnp input_0 none all 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none known 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none novel 0 0 0 0.00 0 0.00 + +##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample +CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio +CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 + +##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator +TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio +TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00 0 0 0.00 0 0 0.00 + +##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay +ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites +ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00 NaN NaN 42 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00 NaN NaN 0 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00 NaN NaN 42 0 0 0 0 0 0 0 0 0 + +##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table +VariantSummary CompRod EvalRod JexlExpression Novelty nSamples nProcessedLoci nSNPs TiTvRatio SNPNoveltyRate nSNPsPerSample TiTvRatioPerSample SNPDPPerSample nIndels IndelNoveltyRate nIndelsPerSample IndelDPPerSample nSVs SVNoveltyRate nSVsPerSample +VariantSummary dbsnp input_0 none all 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none known 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none novel 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +
diff -r 981e31193e25dc5db1923ef2d77c88b99347d670 -r 8cf1bb73a24748aea056a0f1e218783dcaac6e1b test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular --- a/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular +++ /dev/null @@ -1,30 +0,0 @@ -##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites -CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate -CompOverlap dbsnp input_0 none all 0 0 0 0.00 0 0.00 -CompOverlap dbsnp input_0 none known 0 0 0 0.00 0 0.00 -CompOverlap dbsnp input_0 none novel 0 0 0 0.00 0 0.00 - -##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample -CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio -CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 -CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 -CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 - -##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator -TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio -TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00 0 0 0.00 0 0 0.00 -TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00 0 0 0.00 0 0 0.00 -TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00 0 0 0.00 0 0 0.00 - -##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay -ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites -ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00 NaN NaN 42 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00 NaN NaN 0 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00 NaN NaN 42 0 0 0 0 0 0 0 0 0 - -##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table -VariantSummary CompRod EvalRod JexlExpression Novelty nSamples nProcessedLoci nSNPs TiTvRatio SNPNoveltyRate nSNPsPerSample TiTvRatioPerSample SNPDPPerSample nIndels IndelNoveltyRate nIndelsPerSample IndelDPPerSample nSVs SVNoveltyRate nSVsPerSample -VariantSummary dbsnp input_0 none all 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 -VariantSummary dbsnp input_0 none known 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 -VariantSummary dbsnp input_0 none novel 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 -
diff -r 981e31193e25dc5db1923ef2d77c88b99347d670 -r 8cf1bb73a24748aea056a0f1e218783dcaac6e1b tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.7"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.8"><description></description><requirements><requirement type="package" version="1.4">gatk</requirement> @@ -13,7 +13,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantEval" - --out "${output_table}" + --out "${output_report}" --num_threads 4 ##hard coded, for now -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout @@ -495,7 +495,7 @@
</inputs><outputs> - <data format="gatkreport" name="output_table" label="${tool.name} on ${on_string} (table)" /> + <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" /><data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /></outputs><tests> @@ -509,7 +509,7 @@ <param name="comp_rod_bind" value="0" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="basic" /> - <output name="output_table" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular" /> + <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" /><output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" /></test></tests>
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