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annotate picard_MarkDuplicates.xml @ 12:a459ead5ab75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author iuc
date Thu, 13 Apr 2017 19:09:04 -0400
parents 41b8d087a2d2
children c7dd8d7946b8
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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1">
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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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21 REMOVE_DUPLICATES='${remove_duplicates}'
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22 ASSUME_SORTED='${assume_sorted}'
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24 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
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26 #import pipes
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27 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
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28 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
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29
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30 # Optional arguments
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31 #if $barcode_tag:
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32 BARCODE_TAG='${barcode_tag}'
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33 #end if
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35 VALIDATION_STRINGENCY='${validation_stringency}'
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36 QUIET=true
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37 VERBOSITY=ERROR
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39 ]]></command>
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40 <inputs>
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41 <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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42 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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43 <param name="comment" type="text" label="Add this comment to BAM dataset"/>
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44 </repeat>
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45 <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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46 <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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48 <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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49 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
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50 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
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51 </param>
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53
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54 <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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55 <sanitizer>
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56 <valid initial="string.printable">
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57 </valid>
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58 </sanitizer>
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59 </param>
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60 <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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61
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62 <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/>
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63
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64 <expand macro="VS" />
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66 </inputs>
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67
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68 <outputs>
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69 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
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70 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
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71 </outputs>
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72
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73 <tests>
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74 <test>
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75 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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76 <param name="comment" value="test-run"/>
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77 <param name="assume_sorted" value="True"/>
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78 <param name="remove_duplicates" value="True"/>
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79 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
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80 <param name="optical_duplicate_pixel_distance" value="100"/>
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81 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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82 <param name="validation_stringency" value="LENIENT"/>
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83 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
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84 </test>
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85 </tests>
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86
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87
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88 <help>
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89
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90 **Purpose**
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91
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92 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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93
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94 @dataset_collections@
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95
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96 @description@
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97
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98 COMMENT=String
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99 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
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100 more times.
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101
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102 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
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103 appropriate flags set. Default value: false.
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104
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105 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read
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106 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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107 These values are used to estimate the rate of optical duplication in order to give a more
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108 accurate estimated library size. Set this option to null to disable optical duplicate
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109 detection. The regular expression should contain three capture groups for the three
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110 variables, in order. It must match the entire read name. Note that if the default regex
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111 is specified, a regex match is not actually done, but instead the read name is split on
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112 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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113 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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114 are assumed to be tile, x and y values. Default value:
3
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115 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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116
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117 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
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118 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
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119 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
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120
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121 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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122 The maximum offset between two duplicte clusters in order to consider them optical
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123 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
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124 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
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125 which case 50-100 is more normal. Default value: 100.
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126
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127 BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.
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128
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129 @more_info@
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130
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131 </help>
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132 </tool>
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133
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134