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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">0</token>
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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 ##set up input files
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12
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13 #set $reference_fasta_filename = "localref.fa"
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14
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15 @handle_reference_source@
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16
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17 picard
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18 CollectWgsMetrics
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19 --INPUT '$escaped_element_identifier'
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20 --OUTPUT '${outFile}'
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21 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
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22 --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}'
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23 --MINIMUM_BASE_QUALITY '${minimum_base_quality}'
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24 --COVERAGE_CAP '${coverage_cap}'
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25
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26 --VALIDATION_STRINGENCY '${validation_stringency}'
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27 --QUIET true
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28 --VERBOSITY ERROR
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29
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30 ]]></command>
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31 <inputs>
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32 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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33 <conditional name="reference_source">
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34 <param name="reference_source_selector" type="select" label="Load reference genome from">
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35 <option value="cached">Local cache</option>
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36 <option value="history">History</option>
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37 </param>
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38 <when value="cached">
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39 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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40 <options from_data_table="all_fasta">
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41 </options>
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42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
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47 </when>
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48 </conditional>
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49 <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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50 <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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51 <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
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52 <expand macro="VS"/>
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53 </inputs>
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54 <outputs>
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55 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="reference_source_selector" value="history"/>
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60 <param name="minimum_mapping_quality" value="20"/>
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61 <param name="minimum_base_quality" value="20"/>
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62 <param name="coverage_cap" value="250"/>
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63 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa"/>
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64 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam"/>
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65 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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66 </test>
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67 </tests>
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68 <help>
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69
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70 .. class:: infomark
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71
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72 **Purpose**
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73
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74 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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75
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76 @dataset_collections@
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77
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78 @description@
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79
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80 MINIMUM_MAPPING_QUALITY=Integer
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81 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
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82
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83 MINIMUM_BASE_QUALITY=Integer
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84 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
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85
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86 COVERAGE_CAP=Integer
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87 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
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88 Default value: 250.
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89
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90 @more_info@
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91
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92 </help>
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93 <expand macro="citations"/>
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94 </tool>