Mercurial > repos > devteam > picard
changeset 24:b9fbec5ac6b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
| author | iuc |
|---|---|
| date | Fri, 31 May 2019 03:21:52 -0400 |
| parents | 1cd1cf786389 |
| children | 7d34178f2812 |
| files | picard_CollectHsMetrics.xml test-data/picard_CollectHsMetrics.baits test-data/picard_CollectHsMetrics.bam test-data/picard_CollectHsMetrics.target test-data/picard_CollectHsMetrics_test1.tab |
| diffstat | 5 files changed, 315 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@"> + <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description> + <macros> + <import>picard_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@java_options@ +@symlink_element_identifier@ + +picard +CollectHsMetrics +INPUT='$escaped_element_identifier' +OUTPUT='${outFile}' +MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality} +MINIMUM_BASE_QUALITY=${minimum_base_quality} +COVERAGE_CAP=${coverage_cap} +CLIP_OVERLAPPING_READS=${clip_overlapping_reads} +BAIT_INTERVALS='${baitFile}' +TARGET_INTERVALS='${targetFile}' +VALIDATION_STRINGENCY=${validation_stringency} +QUIET=true +VERBOSITY=ERROR +@TMPDIR_OPTION@ + ]]></command> + <inputs> + <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> + <param name="baitFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the baits used" help="If empty, upload or convert from BED" /> + <param name="targetFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the targets" help="If empty, upload or convert from BED" /> + <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20" /> + <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20" /> + <param name="coverage_cap" type="integer" value="200" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=200" /> + <param name="clip_overlapping_reads" type="boolean" label="Clip overlapping reads" checked="true" truevalue="true" falsevalue="false" help="CLIP_OVERLAPPING_READS; default=true" /> + <expand macro="VS" /> + </inputs> + <outputs> + <data name="outFile" format="txt" label="${tool.name} on ${on_string}: Summary data" /> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_CollectHsMetrics.bam" ftype="bam" /> + <param name="baitFile" value="picard_CollectHsMetrics.baits" ftype="picard_interval_list" /> + <param name="targetFile" value="picard_CollectHsMetrics.target" ftype="picard_interval_list" /> + <param name="minimum_mapping_quality" value="20" /> + <param name="minimum_base_quality" value="20" /> + <param name="coverage_cap" value="200" /> + <param name="clip_overlapping_reads" value="true" /> + <output name="outFile" file="picard_CollectHsMetrics_test1.tab" lines_diff="6" /> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**Purpose** + +Computes a number of metrics that are useful for evaluating coverage and performance of datasets generated through hybrid-selection. +Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments +such as exome sequencing. + +@dataset_collections@ + +----- + +.. class:: warningmark + +**Obtaining bait and target interval files in Picard interval_list format** + +This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format. +You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries +for sequencing, which can generally be obtained from the kit manufacturer. +If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format +using Picard's **BedToIntervalList** tool, which will also add the required SAM style header. + +@description@ + + MINIMUM_MAPPING_QUALITY=Integer + MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. + + MINIMUM_BASE_QUALITY=Integer + Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. + + COVERAGE_CAP=Integer + CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. + Default value: 200. + CLIP_OVERLAPPING_READS=Boolean + If true, clip overlapping reads, false otherwise. Default value: true. + +@more_info@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /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
--- /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
--- /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 ZERO_CVG_TARGETS_PCT PCT_EXC_DUPE PCT_EXC_MAPQ PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_OFF_TARGET FOLD_80_BASE_PENALTY PCT_TARGET_BASES_1X PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X PCT_TARGET_BASES_40X PCT_TARGET_BASES_50X PCT_TARGET_BASES_100X HS_LIBRARY_SIZE HS_PENALTY_10X HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X AT_DROPOUT GC_DROPOUT HET_SNP_SENSITIVITY HET_SNP_Q SAMPLE LIBRARY READ_GROUP +dataset_2 16569 303 183 0.60396 543 543 543 1 1 543 1 48712 48712 1545 8432 38735 911 0.204816 0.795184 0.154856 5.09901 4.978142 4 11 0.031614 0.018641 1.734388 0 0 0 0 0.008088 0.99146 2.489071 1 0.994536 0.125683 0 0 0 0 0 0 0 0 0 0 0 0 0 0.879902 9 + +## HISTOGRAM java.lang.Integer +coverage_or_base_quality high_quality_coverage_count unfiltered_baseq_count +0 0 0 +1 1 0 +2 71 0 +3 13 0 +4 13 0 +5 24 0 +6 0 0 +7 4 0 +8 12 0 +9 22 0 +10 18 0 +11 5 0 +12 0 0 +13 0 0 +14 0 0 +15 0 0 +16 0 0 +17 0 0 +18 0 0 +19 0 0 +20 0 0 +21 0 0 +22 0 0 +23 0 0 +24 0 0 +25 0 0 +26 0 0 +27 0 0 +28 0 0 +29 0 0 +30 0 0 +31 0 0 +32 0 0 +33 0 6 +34 0 0 +35 0 0 +36 0 0 +37 0 0 +38 0 3 +39 0 1 +40 0 0 +41 0 1 +42 0 0 +43 0 0 +44 0 0 +45 0 0 +46 0 1 +47 0 0 +48 0 0 +49 0 6 +50 0 4 +51 0 2 +52 0 1 +53 0 4 +54 0 4 +55 0 2 +56 0 8 +57 0 4 +58 0 11 +59 0 2 +60 0 14 +61 0 17 +62 0 26 +63 0 20 +64 0 21 +65 0 65 +66 0 125 +67 0 56 +68 0 70 +69 0 69 +70 0 95 +71 0 117 +72 0 156 +73 0 0 +74 0 0 +75 0 0 +76 0 0 +77 0 0 +78 0 0 +79 0 0 +80 0 0 +81 0 0 +82 0 0 +83 0 0 +84 0 0 +85 0 0 +86 0 0 +87 0 0 +88 0 0 +89 0 0 +90 0 0 +91 0 0 +92 0 0 +93 0 0 +94 0 0 +95 0 0 +96 0 0 +97 0 0 +98 0 0 +99 0 0 +100 0 0 +101 0 0 +102 0 0 +103 0 0 +104 0 0 +105 0 0 +106 0 0 +107 0 0 +108 0 0 +109 0 0 +110 0 0 +111 0 0 +112 0 0 +113 0 0 +114 0 0 +115 0 0 +116 0 0 +117 0 0 +118 0 0 +119 0 0 +120 0 0 +121 0 0 +122 0 0 +123 0 0 +124 0 0 +125 0 0 +126 0 0 +127 0 0 +128 0 0 +129 0 0 +130 0 0 +131 0 0 +132 0 0 +133 0 0 +134 0 0 +135 0 0 +136 0 0 +137 0 0 +138 0 0 +139 0 0 +140 0 0 +141 0 0 +142 0 0 +143 0 0 +144 0 0 +145 0 0 +146 0 0 +147 0 0 +148 0 0 +149 0 0 +150 0 0 +151 0 0 +152 0 0 +153 0 0 +154 0 0 +155 0 0 +156 0 0 +157 0 0 +158 0 0 +159 0 0 +160 0 0 +161 0 0 +162 0 0 +163 0 0 +164 0 0 +165 0 0 +166 0 0 +167 0 0 +168 0 0 +169 0 0 +170 0 0 +171 0 0 +172 0 0 +173 0 0 +174 0 0 +175 0 0 +176 0 0 +177 0 0 +178 0 0 +179 0 0 +180 0 0 +181 0 0 +182 0 0 +183 0 0 +184 0 0 +185 0 0 +186 0 0 +187 0 0 +188 0 0 +189 0 0 +190 0 0 +191 0 0 +192 0 0 +193 0 0 +194 0 0 +195 0 0 +196 0 0 +197 0 0 +198 0 0 +199 0 0 +200 0 0 +