| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/3.1.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2 |
| picard_CollectHsMetrics |
| 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' '$escaped_element_identifier' &&
picard CollectHsMetrics
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
--MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality}
--MINIMUM_BASE_QUALITY ${minimum_base_quality}
--COVERAGE_CAP ${coverage_cap}
--CLIP_OVERLAPPING_READS ${clip_overlapping_reads}
--BAIT_INTERVALS '${baitFile}'
--TARGET_INTERVALS '${targetFile}'
--VALIDATION_STRINGENCY ${validation_stringency}
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_CollectHsMetrics.bam baitFile: picard_CollectHsMetrics.baits targetFile: picard_CollectHsMetrics.target minimum_mapping_quality: 20 minimum_base_quality: 20 coverage_cap: 200 clip_overlapping_reads: True |
name: value |
picard_CollectHsMetrics.bam picard_CollectHsMetrics.baits picard_CollectHsMetrics.target value |