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annotate picard_MeanQualityByCycle.xml @ 3:52fdfc45590a draft

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author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.0">
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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 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.1.2">R</requirement>
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8 </expand>
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9 <command>
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10 @java_options@
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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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15 #if str( $reference_source.reference_source_selector ) == "history":
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16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
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17 #else:
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18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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19 #end if
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21 java -jar \$JAVA_JAR_PATH/picard.jar
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22 MeanQualityByCycle
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23 INPUT="${inputFile}"
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24 OUTPUT="${outFile}"
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25 CHART_OUTPUT="${pdfFile}"
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26 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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27 ALIGNED_READS_ONLY="${aligned_reads_only}"
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28 PF_READS_ONLY="${pf_reads_only}"
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29
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30 ASSUME_SORTED="${assume_sorted}"
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32 VALIDATION_STRINGENCY="${validation_stringency}"
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33 QUIET=true
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34 VERBOSITY=ERROR
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35
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36 </command>
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37 <inputs>
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38 <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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39 <conditional name="reference_source">
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40 <param name="reference_source_selector" type="select" label="Load reference genome from">
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41 <option value="cached">Local cache</option>
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42 <option value="history">History</option>
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43 </param>
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44 <when value="cached">
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45 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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46 <options from_data_table="all_fasta">
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47 </options>
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48 <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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49 </param>
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50 </when>
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51 <when value="history">
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52 <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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53 </when>
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54 </conditional>
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55 <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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56 <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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57 <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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58
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59 <expand macro="VS" />
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61 </inputs>
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62
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63 <outputs>
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64 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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65 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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66 </outputs>
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67
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68 <tests>
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69 <test>
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70 <param name="assume_sorted" value="true" />
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71 <param name="aligned_reads_only" value="false" />
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72 <param name="pf_reads_only" 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_MeanQualityByCycle_ref.fa" />
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75 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
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76 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
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77 </test>
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78 </tests>
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79
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80 <stdio>
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81 <exit_code range="1:" level="fatal"/>
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82 </stdio>
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83
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84 <help>
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85
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86 .. class:: infomark
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87
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88 **Purpose**
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89
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90 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
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91
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92 @dataset_collections@
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93
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94 @description@
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95
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96 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
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97 false. Possible values: {true, false}
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98
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99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
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100 This option can be set to 'null' to clear the default value. Possible values: {true,
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101 false}
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102
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103 ASSUME_SORTED=Boolean
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104 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
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105
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106 @more_info@
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107
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108 </help>
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109 </tool>
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110
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111