# HG changeset patch # User iuc # Date 1559287312 14400 # Node ID b9fbec5ac6b23b6a7695bf2ccc4e83b4b202e6e0 # Parent 1cd1cf7863899e225c5ae75ae7f76d2772873d9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4 diff -r 1cd1cf786389 -r b9fbec5ac6b2 picard_CollectHsMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectHsMetrics.xml Fri May 31 03:21:52 2019 -0400 @@ -0,0 +1,92 @@ + + + compute metrics about datasets generated through hybrid-selection (e.g. exome) + + picard_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 1cd1cf786389 -r b9fbec5ac6b2 test-data/picard_CollectHsMetrics.baits --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectHsMetrics.baits Fri May 31 03:21:52 2019 -0400 @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:coordinate +@SQ SN:chrM LN:16569 +chrM 3100 3200 + NA +chrM 3400 3500 + NA +chrM 3700 3800 + NA diff -r 1cd1cf786389 -r b9fbec5ac6b2 test-data/picard_CollectHsMetrics.bam Binary file test-data/picard_CollectHsMetrics.bam has changed diff -r 1cd1cf786389 -r b9fbec5ac6b2 test-data/picard_CollectHsMetrics.target --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectHsMetrics.target Fri May 31 03:21:52 2019 -0400 @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:coordinate +@SQ SN:chrM LN:16569 +chrM 3120 3180 + NA +chrM 3420 3480 + NA +chrM 3720 3780 + NA diff -r 1cd1cf786389 -r b9fbec5ac6b2 test-data/picard_CollectHsMetrics_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectHsMetrics_test1.tab Fri May 31 03:21:52 2019 -0400 @@ -0,0 +1,213 @@ +## htsjdk.samtools.metrics.StringHeader +# CollectHsMetrics BAIT_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_2.dat] TARGET_INTERVALS=[/tmp/tmpMGxxyd/files/000/dataset_3.dat] INPUT=picard_CollectHsMetrics_bam OUTPUT=/tmp/tmpMGxxyd/files/000/dataset_4.dat MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 TMP_DIR=[/tmp] VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 SAMPLE_SIZE=10000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu May 30 21:41:26 UTC 2019 + +## METRICS CLASS picard.analysis.directed.HsMetrics +BAIT_SET GENOME_SIZE BAIT_TERRITORY TARGET_TERRITORY BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED PF_BASES_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE MEDIAN_TARGET_COVERAGE MAX_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT 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