annotate picard_MarkDuplicatesWithMateCigar.xml @ 23:1cd1cf786389 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:13:32 -0400
parents 6f9c0884a3e7
children 881d7645d1bf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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>
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 </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
7 <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
8 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 @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
10 @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
11 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 MarkDuplicatesWithMateCigar
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
14 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
16
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 METRICS_FILE="${metrics_file}"
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
18 COMMENT="${comment}"
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 6
diff changeset
19
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 MINIMUM_DISTANCE="${minimum_distance}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 SKIP_PAIRS_WITH_NO_MATE_CIGAR="${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
22
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
23
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 REMOVE_DUPLICATES="${remove_duplicates}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 ASSUME_SORTED="${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
26
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
28
21
6f9c0884a3e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
iuc
parents: 20
diff changeset
29 READ_NAME_REGEX='${ str( $read_name_regex ) }'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${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
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
37 @TMPDIR_OPTION@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
38
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
39 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <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
42 <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
43
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <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
45 <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
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <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
50 <option value="TOTAL_MAPPED_REFERENCE_LENGTH" selected="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
55 <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]+).*.">
21
6f9c0884a3e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
iuc
parents: 20
diff changeset
56 <expand macro="sanitize_query" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 <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
61
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
62 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
63
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
68
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="minimum_distance" value="-1"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="skip_pairs_with_no_mate_cigar" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="comment" value="test-run"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="assume_sorted" value="True"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="remove_duplicates" value="False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <param name="optical_duplicate_pixel_distance" value="100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 <param name="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
84
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
85
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 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
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 .. class:: warningmark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 From Samtools Announce MailingList_:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101 (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 alignments that have large gaps or reference skips, which happens frequently in RNA-seq data.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 .. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
109 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
111 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
112 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
113 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
114 default value.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
115
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
116 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
117 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
118 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
119 {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
120
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
121 COMMENT=String
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
122 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
123 more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
124
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
125 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
126 appropriate flags set. Default value: false.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
127
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
128 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
129 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
130 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
131 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
132 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
133 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
134 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
135 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
136 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
137 are assumed to be tile, x and y values. Default value:
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
138 [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
139
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
140 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
141 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
142 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
143
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
144 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
145 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
146 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
147 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
148 which case 50-100 is more normal. Default value: 100.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
149
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
150 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
151
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
152 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
153 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
154 </tool>