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annotate picard_MeanQualityByCycle.xml @ 33:3f254c5ced1d draft default tip

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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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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>chart distribution of base qualities</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">
8
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @java_options@
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11 ##set up input files
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12 @symlink_element_identifier@
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13 #set $reference_fasta_filename = "localref.fa"
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15 @handle_reference_source@
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17 picard MeanQualityByCycle
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18 --INPUT '$escaped_element_identifier'
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19 --OUTPUT '${outFile}'
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20 --CHART_OUTPUT '${pdfFile}'
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21 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
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22 --ALIGNED_READS_ONLY '${aligned_reads_only}'
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23 --PF_READS_ONLY '${pf_reads_only}'
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25 --ASSUME_SORTED '${assume_sorted}'
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27 --VALIDATION_STRINGENCY '${validation_stringency}'
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28 --QUIET true
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29 --VERBOSITY ERROR
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31 ]]></command>
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32 <inputs>
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33 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
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34 <conditional name="reference_source">
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35 <param name="reference_source_selector" type="select" label="Load reference genome from">
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36 <option value="cached">Local cache</option>
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37 <option value="history">History</option>
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38 </param>
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39 <when value="cached">
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40 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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41 <options from_data_table="all_fasta">
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42 </options>
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43 <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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44 </param>
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45 </when>
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46 <when value="history">
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47 <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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48 </when>
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49 </conditional>
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50 <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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51 <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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52 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
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53 <expand macro="VS"/>
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54 </inputs>
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55 <outputs>
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56 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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57 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="assume_sorted" value="true"/>
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62 <param name="aligned_reads_only" value="false"/>
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63 <param name="pf_reads_only" value="false"/>
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64 <param name="reference_source_selector" value="history"/>
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65 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa"/>
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66 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam"/>
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67 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
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68 </test>
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69 </tests>
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70 <help>
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71
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72 .. class:: infomark
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73
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74 **Purpose**
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75
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76 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
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78 @dataset_collections@
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79
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80 @description@
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81
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82 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
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83 false. Possible values: {true, false}
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84
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85 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
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86 This option can be set to 'null' to clear the default value. Possible values: {true,
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87 false}
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88
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89 ASSUME_SORTED=Boolean
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90 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
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91
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92 @more_info@
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93
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94 </help>
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95 <expand macro="citations"/>
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96 </tool>