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 |