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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="1.126.0">
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2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13
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14 java -jar \$JAVA_JAR_PATH/picard.jar
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15 MarkDuplicates
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16
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17 INPUT="${inputFile}"
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18 OUTPUT="${outFile}"
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19
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20 METRICS_FILE="${metrics_file}"
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21 #for $element in $comments:
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22 COMMENT="${element.comment}"
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23 #end for
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24 REMOVE_DUPLICATES="${remove_duplicates}"
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25 ASSUME_SORTED="${assume_sorted}"
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26
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27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
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28
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6
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29 #import pipes
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30 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
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31 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
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32
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33 VALIDATION_STRINGENCY="${validation_stringency}"
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34 QUIET=true
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35 VERBOSITY=ERROR
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36
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37 </command>
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38 <inputs>
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39 <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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40 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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41 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset"/>
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42 </repeat>
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43 <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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44 <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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45
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46 <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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47 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
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48 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
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49 </param>
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50
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51
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52 <param name="read_name_regex" type="text" size="40" 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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53 <sanitizer>
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54 <valid initial="string.printable">
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55 </valid>
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56 </sanitizer>
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57 </param>
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58 <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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59
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60 <expand macro="VS" />
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61
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62 </inputs>
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63
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64 <outputs>
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65 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
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66 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
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67 </outputs>
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68
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69 <tests>
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70 <test>
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71 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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72 <param name="comment" value="test-run"/>
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73 <param name="assume_sorted" value="True"/>
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74 <param name="remove_duplicates" value="True"/>
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75 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
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76 <param name="optical_duplicate_pixel_distance" value="100"/>
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77 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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78 <param name="validation_stringency" value="LENIENT"/>
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79 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="2"/>
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80 </test>
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81 </tests>
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82
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83 <stdio>
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84 <exit_code range="1:" level="fatal"/>
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85 </stdio>
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86
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87 <help>
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88
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89 **Purpose**
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90
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91 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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92
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93 @dataset_collections@
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94
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95 @description@
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96
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97 COMMENT=String
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98 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
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99 more times.
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100
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101 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
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102 appropriate flags set. Default value: false.
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103
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104 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read
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105 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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106 These values are used to estimate the rate of optical duplication in order to give a more
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107 accurate estimated library size. Set this option to null to disable optical duplicate
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108 detection. The regular expression should contain three capture groups for the three
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109 variables, in order. It must match the entire read name. Note that if the default regex
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110 is specified, a regex match is not actually done, but instead the read name is split on
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111 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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112 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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113 are assumed to be tile, x and y values. Default value:
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114 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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115
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116 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
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117 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
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118 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
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119
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120 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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121 The maximum offset between two duplicte clusters in order to consider them optical
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122 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
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123 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
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124 which case 50-100 is more normal. Default value: 100.
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125
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126 @more_info@
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127
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128 </help>
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129 </tool>
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130
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131
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