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annotate picard_MarkDuplicates.xml @ 14:465cbb0cf2eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
author devteam
date Wed, 07 Dec 2016 14:56:30 -0500
parents 7e6fd3d0f16e
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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0">
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2 <description>examine aligned records in BAM datasets to locate duplicate molecules</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 <command detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 @symlink_element_identifier@
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10 picard
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11 MarkDuplicates
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13 INPUT='$escaped_element_identifier'
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14 OUTPUT="${outFile}"
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16 METRICS_FILE="${metrics_file}"
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17 #for $element in $comments:
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18 COMMENT="${element.comment}"
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19 #end for
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20 REMOVE_DUPLICATES="${remove_duplicates}"
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21 ASSUME_SORTED="${assume_sorted}"
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22
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23 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
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24
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25 #import pipes
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26 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
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27 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
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28
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29 VALIDATION_STRINGENCY="${validation_stringency}"
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30 QUIET=true
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31 VERBOSITY=ERROR
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33 ]]></command>
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34 <inputs>
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35 <param format="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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36 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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37 <param name="comment" type="text" label="Add this comment to BAM dataset"/>
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38 </repeat>
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39 <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/>
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40 <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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41
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42 <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=SUM_OF_BASE_QUALITIES">
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43 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
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44 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
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45 </param>
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48 <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
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49 <sanitizer>
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50 <valid initial="string.printable">
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51 </valid>
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52 </sanitizer>
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53 </param>
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54 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
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55
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56 <expand macro="VS" />
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58 </inputs>
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59
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60 <outputs>
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61 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
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62 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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68 <param name="comment" value="test-run"/>
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69 <param name="assume_sorted" value="True"/>
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70 <param name="remove_duplicates" value="True"/>
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71 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
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72 <param name="optical_duplicate_pixel_distance" value="100"/>
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73 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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74 <param name="validation_stringency" value="LENIENT"/>
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75 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
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76 </test>
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77 </tests>
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79
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80 <help>
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81
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82 **Purpose**
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83
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84 Examines aligned records in the supplied SAM or BAM dataset to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged.
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85
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86 @dataset_collections@
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87
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88 @description@
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89
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90 COMMENT=String
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91 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
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92 more times.
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94 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
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95 appropriate flags set. Default value: false.
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96
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97 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read
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98 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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99 These values are used to estimate the rate of optical duplication in order to give a more
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100 accurate estimated library size. Set this option to null to disable optical duplicate
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101 detection. The regular expression should contain three capture groups for the three
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102 variables, in order. It must match the entire read name. Note that if the default regex
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103 is specified, a regex match is not actually done, but instead the read name is split on
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104 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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105 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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106 are assumed to be tile, x and y values. Default value:
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107 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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108
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109 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
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110 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
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111 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
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112
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113 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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114 The maximum offset between two duplicte clusters in order to consider them optical
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115 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
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116 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
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117 which case 50-100 is more normal. Default value: 100.
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118
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119 @more_info@
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120
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121 </help>
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122 </tool>
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