picard: picard_MarkDuplicatesWithMateCigar.xml annotate

annotate picard_MarkDuplicatesWithMateCigar.xml @ 20:2a17c789e0a5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a

author	iuc
date	Tue, 19 Jun 2018 11:28:49 -0400
parents	5053a18d9bc8
children	6f9c0884a3e7

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="${duplicate_scoring_strategy}"
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	28
6 4ff1e04010e6 Uploaded devteam parents: 5 diff changeset	29 #import pipes
4ff1e04010e6 Uploaded devteam parents: 5 diff changeset	30 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	31 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${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	32
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	33
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	34 BLOCK_SIZE=100000
3d4f1fa26f0e Uploaded devteam parents: diff changeset	35 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	36 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: diff changeset	37 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	38 @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	39
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 9 diff changeset	40 ]]></command>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	41 <inputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	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"/>
9 5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1 devteam parents: 8 diff changeset	43 <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	44
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	45 <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	46 <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	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"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	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"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	49
3d4f1fa26f0e Uploaded devteam parents: diff changeset	50 <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	51 <option value="TOTAL_MAPPED_REFERENCE_LENGTH" selected="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	52 <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	53 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	54
3d4f1fa26f0e Uploaded devteam parents: diff changeset	55
9 5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1 devteam parents: 8 diff changeset	56 <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	57 <sanitizer>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	58 <valid initial="string.printable">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	59 </valid>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	60 </sanitizer>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	61 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	62 <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	63
3d4f1fa26f0e Uploaded devteam parents: diff changeset	64 <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	65
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	66 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	67
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	68 <outputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	69 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	70 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	71 </outputs>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	72
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	73 <tests>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	74 <test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	75 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	76 <param name="minimum_distance" value="-1"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	77 <param name="skip_pairs_with_no_mate_cigar" value="True"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	78 <param name="comment" value="test-run"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	79 <param name="assume_sorted" value="True"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	80 <param name="remove_duplicates" value="False"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	81 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	82 <param name="optical_duplicate_pixel_distance" value="100"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	83 <param name="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	84 <param name="validation_stringency" value="LENIENT"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	85 <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	86 </test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	87 </tests>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	88
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	89
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	90 <help>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	91
3d4f1fa26f0e Uploaded devteam parents: diff changeset	92 Purpose
3d4f1fa26f0e Uploaded devteam parents: diff changeset	93
3d4f1fa26f0e Uploaded devteam parents: diff changeset	94 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	95
3d4f1fa26f0e Uploaded devteam parents: diff changeset	96 ------
3d4f1fa26f0e Uploaded devteam parents: diff changeset	97
3d4f1fa26f0e Uploaded devteam parents: diff changeset	98 .. class:: warningmark
3d4f1fa26f0e Uploaded devteam parents: diff changeset	99
3d4f1fa26f0e Uploaded devteam parents: diff changeset	100 On the difference between MarkDuplicates and picard_MarkDuplicatesWithMateCigar
3d4f1fa26f0e Uploaded devteam parents: diff changeset	101
3d4f1fa26f0e Uploaded devteam parents: diff changeset	102 From Samtools Announce MailingList_:
3d4f1fa26f0e Uploaded devteam parents: diff changeset	103
3d4f1fa26f0e Uploaded devteam parents: diff changeset	104 This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed
3d4f1fa26f0e Uploaded devteam parents: diff changeset	105 (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool
3d4f1fa26f0e Uploaded devteam parents: diff changeset	106 to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with
3d4f1fa26f0e Uploaded devteam parents: diff changeset	107 alignments that have large gaps or reference skips, which happens frequently in RNA-seq data.
3d4f1fa26f0e Uploaded devteam parents: diff changeset	108
3d4f1fa26f0e Uploaded devteam parents: diff changeset	109 .. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/
3d4f1fa26f0e Uploaded devteam parents: diff changeset	110
3d4f1fa26f0e Uploaded devteam parents: diff changeset	111 @dataset_collections@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	112
3d4f1fa26f0e Uploaded devteam parents: diff changeset	113 @description@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	114
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	115 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	116 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	117 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	118 default value.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	119
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	120 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	121 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	122 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	123 {true, false}
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	124
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	125 COMMENT=String
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	126 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	127 more times.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	128
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	129 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	130 appropriate flags set. Default value: false.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	131
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	132 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	133 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	134 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	135 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	136 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	137 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	138 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	139 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	140 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	141 are assumed to be tile, x and y values. Default value:
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	142 [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	143
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	144 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	145 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	146 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	147
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	148 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	149 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	150 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	151 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	152 which case 50-100 is more normal. Default value: 100.
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	153
3d4f1fa26f0e Uploaded devteam parents: diff changeset	154 @more_info@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	155
3d4f1fa26f0e Uploaded devteam parents: diff changeset	156 </help>
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	157 <expand macro="citations" />
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	158 </tool>

Mercurial > repos > devteam > picard

annotate picard_MarkDuplicatesWithMateCigar.xml @ 20:2a17c789e0a5 draft