Mercurial > repos > devteam > picard
changeset 18:7615ac66c6e5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
| author | iuc |
|---|---|
| date | Sat, 20 Jan 2018 08:28:24 -0500 |
| parents | fc288950c3b7 |
| children | 5053a18d9bc8 |
| files | picard_MarkDuplicates.xml test-data/picard_MarkDuplicates_test2.bam |
| diffstat | 2 files changed, 29 insertions(+), 13 deletions(-) [+] |
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--- a/picard_MarkDuplicates.xml Thu Apr 13 19:09:24 2017 -0400 +++ b/picard_MarkDuplicates.xml Sat Jan 20 08:28:24 2018 -0500 @@ -1,4 +1,4 @@ -<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1"> +<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.2"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> @@ -24,12 +24,14 @@ DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' #import pipes - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } + #if $read_name_regex: + READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) } + #end if OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' # Optional arguments #if $barcode_tag: - BARCODE_TAG='${barcode_tag}' + BARCODE_TAG='${barcode_tag}' #end if VALIDATION_STRINGENCY='${validation_stringency}' @@ -50,8 +52,8 @@ <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</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]+).*."> + <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)"> + <sanitizer> <valid initial="string.printable"> </valid> @@ -76,12 +78,23 @@ <param name="comment" value="test-run"/> <param name="assume_sorted" value="True"/> <param name="remove_duplicates" value="True"/> - <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> + <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="SUM_OF_BASE_QUALITIES"/> <param name="validation_stringency" value="LENIENT"/> <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/> </test> + <test> + <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> + <param name="comment" value="test-run"/> + <param name="assume_sorted" value="True"/> + <param name="remove_duplicates" value="False"/> + <param name="read_name_regex" value=""/> + <param name="optical_duplicate_pixel_distance" value="100"/> + <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/> + </test> </tests> @@ -102,7 +115,9 @@ 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 + READ_NAME_REGEX=String This option is only needed if your read names do not follow a standard illumina convention + of colon separation but do contain tile, x, and y coordinates (unusual). + A 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 @@ -111,18 +126,19 @@ 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]+).*. + are assumed to be tile, x and y values. Default value: '' + DUPLICATE_SCORING_STRATEGY=ScoringStrategy DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: SUM_OF_BASE_QUALITIES. 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. + The maximum offset between two duplicate clusters in order to consider them optical + duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells. + Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500. + For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels) + Default value: 100. BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.