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view picard_MarkDuplicatesWithMateCigar.xml @ 26:fc3866ddc7b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author | iuc |
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date | Mon, 22 Aug 2022 09:54:37 +0000 |
parents | e65f2d5fd3d8 |
children | fdca9493e09b |
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<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ picard MarkDuplicatesWithMateCigar INPUT='$escaped_element_identifier' OUTPUT="${outFile}" METRICS_FILE="${metrics_file}" COMMENT="${comment}" MINIMUM_DISTANCE="${minimum_distance}" SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}" REMOVE_DUPLICATES="${remove_duplicates}" ASSUME_SORTED="${assume_sorted}" DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" READ_NAME_REGEX='${ str( $read_name_regex ) }' OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" BLOCK_SIZE=100000 VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR @TMPDIR_OPTION@ ]]></command> <inputs> <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"/> <param name="comment" type="text" label="Add this comment to BAM dataset"/> <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"/> <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"/> <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"/> <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"/> <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"> <option value="TOTAL_MAPPED_REFERENCE_LENGTH" selected="True">TOTAL_MAPPED_REFERENCE_LENGTH</option> <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> </param> <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]+).*."> <expand macro="sanitize_query" /> </param> <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"/> <expand macro="VS" /> </inputs> <outputs> <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> </outputs> <tests> <test> <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/> <param name="minimum_distance" value="-1"/> <param name="skip_pairs_with_no_mate_cigar" value="True"/> <param name="comment" value="test-run"/> <param name="assume_sorted" value="True"/> <param name="remove_duplicates" value="False"/> <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> <param name="optical_duplicate_pixel_distance" value="100"/> <param name="duplicate_scoring_strategy" value="TOTAL_MAPPED_REFERENCE_LENGTH"/> <param name="validation_stringency" value="LENIENT"/> <output name="outFile" file="picard_MarkDuplicatesWithMateCigar_test1.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help> **Purpose** 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. ------ .. class:: warningmark On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar** From Samtools Announce MailingList_: This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with alignments that have large gaps or reference skips, which happens frequently in RNA-seq data. .. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/ @dataset_collections@ @description@ MINIMUM_DISTANCE=Integer The minimum distance to buffer records to account for clipping on the 5' end of the records.Set this number to -1 to use twice the first read's read length (or 100, whichever is smaller). Default value: -1. This option can be set to 'null' to clear the default value. SKIP_PAIRS_WITH_NO_MATE_CIGAR=Boolean Skip record pairs with no mate cigar and include them in the output. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false} COMMENT=String CO=String Comment(s) to include in the output file's header. This option may be specified 0 or more times. REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with appropriate flags set. Default value: false. READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. 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. Set this option to null to disable optical duplicate detection. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. DUPLICATE_SCORING_STRATEGY=ScoringStrategy DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: TOTAL_MAPPED_REFERENCE_LENGTH. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100. @more_info@ </help> <expand macro="citations" /> </tool>