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annotate picard_QualityScoreDistribution.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 2a17c789e0a5
children 3f254c5ced1d
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1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>chart quality score distribution</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@">1</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.4.1">r-base</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @java_options@
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12 ##set up input files
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13 @symlink_element_identifier@
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14 #set $reference_fasta_filename = "localref.fa"
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16 @handle_reference_source@
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18 picard
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19 QualityScoreDistribution
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20 INPUT='$escaped_element_identifier'
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21 OUTPUT="${outFile}"
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22 CHART_OUTPUT="${pdfFile}"
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23 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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24 ALIGNED_READS_ONLY="${aligned_reads_only}"
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25 PF_READS_ONLY="${pf_reads_only}"
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26 INCLUDE_NO_CALLS="${include_no_calls}"
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27
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28 ASSUME_SORTED="${assume_sorted}"
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29
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30 VALIDATION_STRINGENCY="${validation_stringency}"
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31 QUIET=true
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32 VERBOSITY=ERROR
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33
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34 ]]></command>
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35 <inputs>
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36 <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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37 <conditional name="reference_source">
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38 <param name="reference_source_selector" type="select" label="Load reference genome from">
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39 <option value="cached">Local cache</option>
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40 <option value="history">History</option>
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41 </param>
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42 <when value="cached">
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43 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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44 <options from_data_table="all_fasta">
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45 </options>
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46 <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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47 </param>
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48 </when>
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49 <when value="history">
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50 <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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51 </when>
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52 </conditional>
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53 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
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54 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
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55 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
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56 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
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57
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58 <expand macro="VS" />
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59
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60 </inputs>
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61
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62 <outputs>
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63 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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64 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <param name="assume_sorted" value="true" />
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70 <param name="aligned_reads_only" value="false" />
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71 <param name="pf_reads_only" value="false" />
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72 <param name="include_no_calls" value="false" />
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73 <param name="reference_source_selector" value="history" />
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74 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
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75 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
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76 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
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77 </test>
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78 </tests>
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80
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81 <help>
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82
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83 .. class:: infomark
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84
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85 **Purpose**
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86
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87 Program to chart quality score distributions in a SAM or BAM dataset.
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88
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89 @dataset_collections@
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90
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91 @description@
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92
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93 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
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94 false. Possible values: {true, false}
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95
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96 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
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97 Possible values: {true, false}
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99 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
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100 false. Possible values: {true, false}
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101
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102 ASSUME_SORTED=Boolean
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103 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
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104
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105 @more_info@
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106
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107 </help>
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108 <expand macro="citations" />
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109 </tool>