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annotate picard_CollectHsMetrics.xml @ 26:9ffcddf6f9c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author iuc
date Mon, 17 Feb 2020 10:24:29 -0500
parents b9fbec5ac6b2
children f9242e01365a
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
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3 <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
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4 <macros>
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5 <import>picard_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11
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12 picard
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13 CollectHsMetrics
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14 INPUT='$escaped_element_identifier'
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15 OUTPUT='${outFile}'
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16 MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality}
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17 MINIMUM_BASE_QUALITY=${minimum_base_quality}
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18 COVERAGE_CAP=${coverage_cap}
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19 CLIP_OVERLAPPING_READS=${clip_overlapping_reads}
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20 BAIT_INTERVALS='${baitFile}'
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21 TARGET_INTERVALS='${targetFile}'
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22 VALIDATION_STRINGENCY=${validation_stringency}
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23 QUIET=true
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24 VERBOSITY=ERROR
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25 @TMPDIR_OPTION@
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26 ]]></command>
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27 <inputs>
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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" />
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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" />
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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" />
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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" />
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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" />
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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" />
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34 <param name="clip_overlapping_reads" type="boolean" label="Clip overlapping reads" checked="true" truevalue="true" falsevalue="false" help="CLIP_OVERLAPPING_READS; default=true" />
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35 <expand macro="VS" />
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36 </inputs>
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37 <outputs>
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38 <data name="outFile" format="txt" label="${tool.name} on ${on_string}: Summary data" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="inputFile" value="picard_CollectHsMetrics.bam" ftype="bam" />
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43 <param name="baitFile" value="picard_CollectHsMetrics.baits" ftype="picard_interval_list" />
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44 <param name="targetFile" value="picard_CollectHsMetrics.target" ftype="picard_interval_list" />
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45 <param name="minimum_mapping_quality" value="20" />
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46 <param name="minimum_base_quality" value="20" />
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47 <param name="coverage_cap" value="200" />
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48 <param name="clip_overlapping_reads" value="true" />
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49 <output name="outFile" file="picard_CollectHsMetrics_test1.tab" lines_diff="6" />
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 .. class:: infomark
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54
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55 **Purpose**
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56
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57 Computes a number of metrics that are useful for evaluating coverage and performance of datasets generated through hybrid-selection.
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58 Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments
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59 such as exome sequencing.
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60
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61 @dataset_collections@
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62
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63 -----
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64
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65 .. class:: warningmark
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66
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67 **Obtaining bait and target interval files in Picard interval_list format**
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68
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69 This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format.
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70 You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries
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71 for sequencing, which can generally be obtained from the kit manufacturer.
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72 If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format
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73 using Picard's **BedToIntervalList** tool, which will also add the required SAM style header.
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74
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75 @description@
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76
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77 MINIMUM_MAPPING_QUALITY=Integer
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78 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
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79
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80 MINIMUM_BASE_QUALITY=Integer
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81 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
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82
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83 COVERAGE_CAP=Integer
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84 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
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85 Default value: 200.
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
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parents:
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86 CLIP_OVERLAPPING_READS=Boolean
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
iuc
parents:
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87 If true, clip overlapping reads, false otherwise. Default value: true.
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
iuc
parents:
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88
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
iuc
parents:
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89 @more_info@
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
iuc
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90 ]]></help>
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
iuc
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91 <expand macro="citations" />
b9fbec5ac6b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
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92 </tool>