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annotate picard_MarkDuplicates.xml @ 25:7d34178f2812 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
author iuc
date Tue, 11 Jun 2019 02:36:54 -0400
parents 6f9c0884a3e7
children 881d7645d1bf
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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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 <token name="@WRAPPER_VERSION@">2</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11 picard
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12 MarkDuplicates
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14 INPUT='$escaped_element_identifier'
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15 OUTPUT='${outFile}'
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17 METRICS_FILE='${metrics_file}'
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18 #for $element in $comments:
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19 COMMENT='${element.comment}'
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20 #end for
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22 REMOVE_DUPLICATES='${remove_duplicates}'
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23 ASSUME_SORTED='${assume_sorted}'
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25 DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
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27 #if $read_name_regex:
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28 READ_NAME_REGEX='${ str( $read_name_regex ) }'
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29 #end if
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30 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
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32 #if $barcode_tag:
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33 BARCODE_TAG='${barcode_tag}'
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34 #end if
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36 VALIDATION_STRINGENCY='${validation_stringency}'
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37 QUIET=true
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38 VERBOSITY=ERROR
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39 @TMPDIR_OPTION@
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41 ]]></command>
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42 <inputs>
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43 <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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44 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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45 <param name="comment" type="text" label="Add this comment to BAM dataset"/>
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46 </repeat>
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47 <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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48 <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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49
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50 <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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51 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
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52 <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option>
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53 </param>
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54
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55 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)">
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56 <expand macro="sanitize_query" />
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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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60 <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. Typically 'RX' "/>
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61
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62 <expand macro="VS" />
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64 </inputs>
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65
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66 <outputs>
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67 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
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68 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
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69 </outputs>
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70
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71 <tests>
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72 <test>
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73 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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74 <param name="comment" value="test-run"/>
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75 <param name="assume_sorted" value="True"/>
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76 <param name="remove_duplicates" value="True"/>
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77 <param name="read_name_regex" value=".*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*"/>
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78 <param name="optical_duplicate_pixel_distance" value="100"/>
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79 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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80 <param name="validation_stringency" value="LENIENT"/>
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81 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
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82 </test>
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83 <test>
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84 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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85 <param name="comment" value="test-run"/>
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86 <param name="assume_sorted" value="True"/>
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87 <param name="remove_duplicates" value="False"/>
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88 <param name="read_name_regex" value=""/>
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89 <param name="optical_duplicate_pixel_distance" value="100"/>
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90 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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91 <param name="validation_stringency" value="LENIENT"/>
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92 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
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93 </test>
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94 <test>
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95 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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96 <param name="comment" value="test-run"/>
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97 <param name="assume_sorted" value="True"/>
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98 <param name="remove_duplicates" value="False"/>
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99 <param name="read_name_regex" value=""/>
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100 <param name="optical_duplicate_pixel_distance" value="100"/>
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101 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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102 <param name="validation_stringency" value="LENIENT"/>
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103 <param name='barcode_tag' value="RX"/>
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104 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
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105 </test>
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106 </tests>
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107
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108
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109 <help>
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110
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111 **Purpose**
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112
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113 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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114
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115 @dataset_collections@
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116
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117 @description@
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118
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119 COMMENT=String
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120 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
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121 more times.
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122
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123 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
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124 appropriate flags set. Default value: false.
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125
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126 READ_NAME_REGEX=String This option is only needed if your read names do not follow a standard illumina convention
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127 of colon separation but do contain tile, x, and y coordinates (unusual).
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128 A regular expression that can be used to parse read names in the incoming SAM file. Read
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129 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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130 These values are used to estimate the rate of optical duplication in order to give a more
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131 accurate estimated library size. Set this option to null to disable optical duplicate
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132 detection. The regular expression should contain three capture groups for the three
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133 variables, in order. It must match the entire read name. Note that if the default regex
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134 is specified, a regex match is not actually done, but instead the read name is split on
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135 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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136 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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137 are assumed to be tile, x and y values. Default value: ''
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138
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139
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140 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
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141 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
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142 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
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143
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144 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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145 The maximum offset between two duplicate clusters in order to consider them optical
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146 duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells.
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147 Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500.
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148 For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels)
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149 Default value: 100.
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150
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151 BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.
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152
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153 @more_info@
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154
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155 </help>
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156 <expand macro="citations" />
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157 </tool>