changeset 19:862298bf72d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:17 -0400
parents f8748e3fd865
children c1aaa5a116d0
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(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectHsMetrics.xml	Fri May 31 03:21:17 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 03:21:17 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
Binary file test-data/picard_CollectHsMetrics.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectHsMetrics.target	Fri May 31 03:21:17 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 03:21:17 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
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