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annotate picard_MarkDuplicatesWithMateCigar.xml @ 9:5eaa8a968300 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 17:43:13 -0400 |
| parents | 3a3234d7a2e8 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements" /> |
| 5 | 7 <command> |
| 8 @java_options@ | |
| 9 | |
| 10 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 11 MarkDuplicatesWithMateCigar | |
| 12 | |
| 13 INPUT="${inputFile}" | |
| 14 OUTPUT="${outFile}" | |
| 15 | |
| 16 METRICS_FILE="${metrics_file}" | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
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diff
changeset
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17 COMMENT="${comment}" |
|
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
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diff
changeset
|
18 |
| 5 | 19 MINIMUM_DISTANCE="${minimum_distance}" |
| 20 SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}" | |
| 21 | |
| 22 | |
| 23 REMOVE_DUPLICATES="${remove_duplicates}" | |
| 24 ASSUME_SORTED="${assume_sorted}" | |
| 25 | |
| 26 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" | |
| 27 | |
| 6 | 28 #import pipes |
| 29 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } | |
| 5 | 30 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" |
| 31 | |
| 32 | |
| 33 BLOCK_SIZE=100000 | |
| 34 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 35 QUIET=true | |
| 36 VERBOSITY=ERROR | |
| 37 | |
| 38 </command> | |
| 39 <inputs> | |
| 40 <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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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
|
41 <param name="comment" type="text" label="Add this comment to BAM dataset"/> |
| 5 | 42 |
| 43 <param name="minimum_distance" type="integer" value="-1" label="The minimum distance to buffer records to account for clipping on the 5' end of the records" help="MINIMUM_DISTANCE; Set this number to -1 to use twice the first read's read length (or 100, whichever is smaller); default=-1"/> | |
| 44 <param name="skip_pairs_with_no_mate_cigar" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Skip record pairs with no mate cigar and include them in the output" help="SKIP_PAIRS_WITH_NO_MATE_CIGAR; default=True"/> | |
| 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"/> | |
| 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"/> | |
| 47 | |
| 48 <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=TOTAL_MAPPED_REFERENCE_LENGTH"> | |
| 49 <option value="TOTAL_MAPPED_REFERENCE_LENGTH" select="True">TOTAL_MAPPED_REFERENCE_LENGTH</option> | |
| 50 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> | |
| 51 </param> | |
| 52 | |
| 53 | |
|
9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
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]+).*."> |
| 5 | 55 <sanitizer> |
| 56 <valid initial="string.printable"> | |
| 57 </valid> | |
| 58 </sanitizer> | |
| 59 </param> | |
| 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"/> | |
| 61 | |
| 62 <expand macro="VS" /> | |
| 63 | |
| 64 </inputs> | |
| 65 | |
| 66 <outputs> | |
| 67 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> | |
| 68 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> | |
| 69 </outputs> | |
| 70 | |
| 71 <tests> | |
| 72 <test> | |
| 73 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/> | |
| 74 <param name="minimum_distance" value="-1"/> | |
| 75 <param name="skip_pairs_with_no_mate_cigar" value="True"/> | |
| 76 <param name="comment" value="test-run"/> | |
| 77 <param name="assume_sorted" value="True"/> | |
| 78 <param name="remove_duplicates" value="False"/> | |
| 79 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> | |
| 80 <param name="optical_duplicate_pixel_distance" value="100"/> | |
| 81 <param name="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/> | |
| 82 <param name="validation_stringency" value="LENIENT"/> | |
| 83 <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/> | |
| 84 </test> | |
| 85 </tests> | |
| 86 | |
| 87 <stdio> | |
| 88 <exit_code range="1:" level="fatal"/> | |
| 89 </stdio> | |
| 90 | |
| 91 <help> | |
| 92 | |
| 93 **Purpose** | |
| 94 | |
| 95 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. | |
| 96 | |
| 97 ------ | |
| 98 | |
| 99 .. class:: warningmark | |
| 100 | |
| 101 On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar** | |
| 102 | |
| 103 From Samtools Announce MailingList_: | |
| 104 | |
| 105 This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed | |
| 106 (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool | |
| 107 to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with | |
| 108 alignments that have large gaps or reference skips, which happens frequently in RNA-seq data. | |
| 109 | |
| 110 .. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/ | |
| 111 | |
| 112 @dataset_collections@ | |
| 113 | |
| 114 @description@ | |
| 115 | |
| 116 MINIMUM_DISTANCE=Integer The minimum distance to buffer records to account for clipping on the 5' end of the | |
| 117 records.Set this number to -1 to use twice the first read's read length (or 100, | |
| 118 whichever is smaller). Default value: -1. This option can be set to 'null' to clear the | |
| 119 default value. | |
| 120 | |
| 121 SKIP_PAIRS_WITH_NO_MATE_CIGAR=Boolean | |
| 122 Skip record pairs with no mate cigar and include them in the output. Default value: | |
| 123 true. This option can be set to 'null' to clear the default value. Possible values: | |
| 124 {true, false} | |
| 125 | |
| 126 COMMENT=String | |
| 127 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or | |
| 128 more times. | |
| 129 | |
| 130 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with | |
| 131 appropriate flags set. Default value: false. | |
| 132 | |
| 133 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read | |
| 134 names are parsed to extract three variables: tile/region, x coordinate and y coordinate. | |
| 135 These values are used to estimate the rate of optical duplication in order to give a more | |
| 136 accurate estimated library size. Set this option to null to disable optical duplicate | |
| 137 detection. The regular expression should contain three capture groups for the three | |
| 138 variables, in order. It must match the entire read name. Note that if the default regex | |
| 139 is specified, a regex match is not actually done, but instead the read name is split on | |
| 140 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be | |
| 141 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements | |
| 142 are assumed to be tile, x and y values. Default value: | |
| 143 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. | |
| 144 | |
| 145 DUPLICATE_SCORING_STRATEGY=ScoringStrategy | |
| 146 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: | |
| 147 TOTAL_MAPPED_REFERENCE_LENGTH. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} | |
| 148 | |
| 149 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer | |
| 150 The maximum offset between two duplicte clusters in order to consider them optical | |
| 151 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) | |
| 152 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in | |
| 153 which case 50-100 is more normal. Default value: 100. | |
| 154 | |
| 155 @more_info@ | |
| 156 | |
| 157 </help> | |
| 158 </tool> | |
| 159 | |
| 160 |