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comparison picard_CollectHsMetrics.xml @ 24:b9fbec5ac6b2 draft

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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
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children f9242e01365a
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23:1cd1cf786389 24:b9fbec5ac6b2
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
3 <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
4 <macros>
5 <import>picard_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@
10 @symlink_element_identifier@
11
12 picard
13 CollectHsMetrics
14 INPUT='$escaped_element_identifier'
15 OUTPUT='${outFile}'
16 MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality}
17 MINIMUM_BASE_QUALITY=${minimum_base_quality}
18 COVERAGE_CAP=${coverage_cap}
19 CLIP_OVERLAPPING_READS=${clip_overlapping_reads}
20 BAIT_INTERVALS='${baitFile}'
21 TARGET_INTERVALS='${targetFile}'
22 VALIDATION_STRINGENCY=${validation_stringency}
23 QUIET=true
24 VERBOSITY=ERROR
25 @TMPDIR_OPTION@
26 ]]></command>
27 <inputs>
28 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
29 <param name="baitFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the baits used" help="If empty, upload or convert from BED" />
30 <param name="targetFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the targets" help="If empty, upload or convert from BED" />
31 <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20" />
32 <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20" />
33 <param name="coverage_cap" type="integer" value="200" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=200" />
34 <param name="clip_overlapping_reads" type="boolean" label="Clip overlapping reads" checked="true" truevalue="true" falsevalue="false" help="CLIP_OVERLAPPING_READS; default=true" />
35 <expand macro="VS" />
36 </inputs>
37 <outputs>
38 <data name="outFile" format="txt" label="${tool.name} on ${on_string}: Summary data" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="inputFile" value="picard_CollectHsMetrics.bam" ftype="bam" />
43 <param name="baitFile" value="picard_CollectHsMetrics.baits" ftype="picard_interval_list" />
44 <param name="targetFile" value="picard_CollectHsMetrics.target" ftype="picard_interval_list" />
45 <param name="minimum_mapping_quality" value="20" />
46 <param name="minimum_base_quality" value="20" />
47 <param name="coverage_cap" value="200" />
48 <param name="clip_overlapping_reads" value="true" />
49 <output name="outFile" file="picard_CollectHsMetrics_test1.tab" lines_diff="6" />
50 </test>
51 </tests>
52 <help><![CDATA[
53 .. class:: infomark
54
55 **Purpose**
56
57 Computes a number of metrics that are useful for evaluating coverage and performance of datasets generated through hybrid-selection.
58 Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments
59 such as exome sequencing.
60
61 @dataset_collections@
62
63 -----
64
65 .. class:: warningmark
66
67 **Obtaining bait and target interval files in Picard interval_list format**
68
69 This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format.
70 You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries
71 for sequencing, which can generally be obtained from the kit manufacturer.
72 If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format
73 using Picard's **BedToIntervalList** tool, which will also add the required SAM style header.
74
75 @description@
76
77 MINIMUM_MAPPING_QUALITY=Integer
78 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
79
80 MINIMUM_BASE_QUALITY=Integer
81 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
82
83 COVERAGE_CAP=Integer
84 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
85 Default value: 200.
86 CLIP_OVERLAPPING_READS=Boolean
87 If true, clip overlapping reads, false otherwise. Default value: true.
88
89 @more_info@
90 ]]></help>
91 <expand macro="citations" />
92 </tool>