annotate picard_MarkDuplicatesWithMateCigar.xml @ 13:7e6fd3d0f16e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
6 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
9 @symlink_element_identifier@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
10 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 MarkDuplicatesWithMateCigar
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
12
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13 INPUT='$inputFile.element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 METRICS_FILE="${metrics_file}"
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
17 COMMENT="${comment}"
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
18
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 MINIMUM_DISTANCE="${minimum_distance}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
21
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
22
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 REMOVE_DUPLICATES="${remove_duplicates}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 ASSUME_SORTED="${assume_sorted}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
6
4ff1e04010e6 Uploaded
devteam
parents: 5
diff changeset
28 #import pipes
4ff1e04010e6 Uploaded
devteam
parents: 5
diff changeset
29 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
31
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
32
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 BLOCK_SIZE=100000
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
37
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
38 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
41 <param name="comment" type="text" label="Add this comment to BAM dataset"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
42
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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">
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
49 <option value="TOTAL_MAPPED_REFERENCE_LENGTH" selected="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 <sanitizer>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 <valid initial="string.printable">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 </valid>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 </sanitizer>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
63
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
64 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
65
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
70
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="minimum_distance" value="-1"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="skip_pairs_with_no_mate_cigar" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="comment" value="test-run"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <param name="assume_sorted" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <param name="remove_duplicates" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <param name="optical_duplicate_pixel_distance" value="100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <param name="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
86
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
87
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 .. class:: warningmark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 From Samtools Announce MailingList_:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104 to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 alignments that have large gaps or reference skips, which happens frequently in RNA-seq data.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107 .. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
109 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
111 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
112
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
113 MINIMUM_DISTANCE=Integer The minimum distance to buffer records to account for clipping on the 5' end of the
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
114 records.Set this number to -1 to use twice the first read's read length (or 100,
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
115 whichever is smaller). Default value: -1. This option can be set to 'null' to clear the
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
116 default value.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
117
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
118 SKIP_PAIRS_WITH_NO_MATE_CIGAR=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
119 Skip record pairs with no mate cigar and include them in the output. Default value:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
120 true. This option can be set to 'null' to clear the default value. Possible values:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
121 {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
122
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
123 COMMENT=String
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
124 CO=String Comment(s) to include in the output file's header. This option may be specified 0 or
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
125 more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
126
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
127 REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
128 appropriate flags set. Default value: false.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
129
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
130 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
131 names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
132 These values are used to estimate the rate of optical duplication in order to give a more
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
133 accurate estimated library size. Set this option to null to disable optical duplicate
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
134 detection. The regular expression should contain three capture groups for the three
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
135 variables, in order. It must match the entire read name. Note that if the default regex
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
136 is specified, a regex match is not actually done, but instead the read name is split on
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
137 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
138 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
139 are assumed to be tile, x and y values. Default value:
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
140 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
141
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
142 DUPLICATE_SCORING_STRATEGY=ScoringStrategy
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
143 DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
144 TOTAL_MAPPED_REFERENCE_LENGTH. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
145
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
146 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
147 The maximum offset between two duplicte clusters in order to consider them optical
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
148 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
149 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
150 which case 50-100 is more normal. Default value: 100.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
151
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
152 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
153
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
154 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
155 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
156
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
157