| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/1.126.0 |
| picard_MarkDuplicatesWithMateCigar |
| 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' '$escaped_element_identifier' &&
picard MarkDuplicatesWithMateCigar
--INPUT '$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
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_MarkDuplicatesWithMateCigar.bam comment: test-run minimum_distance: -1 skip_pairs_with_no_mate_cigar: True remove_duplicates: False assume_sorted: True duplicate_scoring_strategy: TOTAL_MAPPED_REFERENCE_LENGTH 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_MarkDuplicatesWithMateCigar.bam value |