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annotate picard_MarkDuplicates.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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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@">0</token>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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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 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 #if $read_name_regex:
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27 --READ_NAME_REGEX '${ str( $read_name_regex ) }'
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28 #end if
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29 --OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}'
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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 --TAGGING_POLICY All
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37 --QUIET true
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38 --VERBOSITY ERROR
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40 ]]></command>
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41 <inputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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42 <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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43 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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44 <param name="comment" type="text" label="Add this comment to BAM dataset"/>
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45 </repeat>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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46 <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"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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47 <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">
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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49 <option value="SUM_OF_BASE_QUALITIES" selected="true">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 <option value="RANDOM">RANDOM</option>
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52 </param>
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53 <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)">
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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54 <expand macro="sanitize_query"/>
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55 </param>
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56 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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57 <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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58 <expand macro="VS"/>
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59 </inputs>
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60 <outputs>
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61 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
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62 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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67 <param name="comment" value="test-run"/>
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68 <param name="assume_sorted" value="True"/>
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69 <param name="remove_duplicates" value="True"/>
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70 <param name="read_name_regex" value=".*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*"/>
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71 <param name="optical_duplicate_pixel_distance" value="100"/>
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72 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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73 <param name="validation_stringency" value="LENIENT"/>
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74 <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
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75 </test>
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76 <test>
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77 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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78 <param name="comment" value="test-run"/>
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79 <param name="assume_sorted" value="True"/>
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80 <param name="remove_duplicates" value="False"/>
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81 <param name="read_name_regex" value=""/>
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82 <param name="optical_duplicate_pixel_distance" value="100"/>
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83 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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84 <param name="validation_stringency" value="LENIENT"/>
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85 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
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86 </test>
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87 <test>
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88 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
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89 <param name="comment" value="test-run"/>
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90 <param name="assume_sorted" value="True"/>
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91 <param name="remove_duplicates" value="False"/>
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92 <param name="read_name_regex" value=""/>
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93 <param name="optical_duplicate_pixel_distance" value="100"/>
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94 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
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95 <param name="validation_stringency" value="LENIENT"/>
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96 <param name="barcode_tag" value="RX"/>
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97 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
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98 </test>
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99 </tests>
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100 <help>
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101
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102 **Purpose**
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103
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104 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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105
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106 @dataset_collections@
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107
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108 @description@
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109
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110 COMMENT=String
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111 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
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112 more times.
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113
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114 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
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115 appropriate flags set. Default value: false.
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116
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117 READ_NAME_REGEX=String This option is only needed if your read names do not follow a standard illumina convention
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118 of colon separation but do contain tile, x, and y coordinates (unusual).
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119 A regular expression that can be used to parse read names in the incoming SAM file. Read
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120 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
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121 These values are used to estimate the rate of optical duplication in order to give a more
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122 accurate estimated library size. Set this option to null to disable optical duplicate
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123 detection. The regular expression should contain three capture groups for the three
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124 variables, in order. It must match the entire read name. Note that if the default regex
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125 is specified, a regex match is not actually done, but instead the read name is split on
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126 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
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127 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
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128 are assumed to be tile, x and y values. Default value: ''
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129
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130
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131 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
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132 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
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133 SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
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134
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135 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
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136 The maximum offset between two duplicate clusters in order to consider them optical
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137 duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells.
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138 Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500.
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139 For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels)
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140 Default value: 100.
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141
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142 BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.
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143
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144 @more_info@
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145
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146 </help>
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147 <expand macro="citations"/>
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148 </tool>