| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0 |
| picard_MarkDuplicates |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 3.1.1 | package |
| Additional information about this tool |
_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
export _JAVA_OPTIONS &&
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier' &&
picard MarkDuplicates
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
--METRICS_FILE '${metrics_file}'
#for $element in $comments:
--COMMENT '${element.comment}'
#end for
--REMOVE_DUPLICATES '${remove_duplicates}'
--ASSUME_SORTED '${assume_sorted}'
--DUPLICATE_SCORING_STRATEGY ${duplicate_scoring_strategy}
#if $read_name_regex:
--READ_NAME_REGEX '${ str( $read_name_regex ) }'
#end if
--OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}'
#if $barcode_tag:
--BARCODE_TAG '${barcode_tag}'
#end if
--VALIDATION_STRINGENCY '${validation_stringency}'
--TAGGING_POLICY All
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_MarkDuplicates.bam comments_0|comment: test-run remove_duplicates: True assume_sorted: True duplicate_scoring_strategy: SUM_OF_BASE_QUALITIES read_name_regex: .*[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* optical_duplicate_pixel_distance: 100 validation_stringency: LENIENT |
name: value |
picard_MarkDuplicates.bam value |
| Test-2 |
inputFile: picard_MarkDuplicates.bam comments_0|comment: test-run remove_duplicates: False assume_sorted: True duplicate_scoring_strategy: SUM_OF_BASE_QUALITIES read_name_regex: optical_duplicate_pixel_distance: 100 validation_stringency: LENIENT |
name: value |
picard_MarkDuplicates.bam value |
| Test-3 |
inputFile: picard_MarkDuplicates.bam comments_0|comment: test-run remove_duplicates: False assume_sorted: True duplicate_scoring_strategy: SUM_OF_BASE_QUALITIES read_name_regex: optical_duplicate_pixel_distance: 100 barcode_tag: RX validation_stringency: LENIENT |
name: value |
picard_MarkDuplicates.bam value |